Programas de bioinformatica instalados:
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Chapter 1. Lista de los programas instalados

La lista siguiente muestra los programas que se instalaron ademas de los por default en el cluster. Checan si el programa que quieren utilizar contiene la columna module llena, o vacia.

Si contiene indicación de un module (por ejemplo el programa Samtools), vean como usar los modulos en la pagina siguiente.

Si no contiene informacion de module (por ejemplo ....), vean la pagina siiguiente "Uso de script file".

Los que necesiten utilizar Python Python o R, revisen las paginas siguientes relativas a estos dos programas, para conocer los paquetes instalados en ellos.

Warning

Revise las paginas siguientes para conocer como usar los programas aqui listados.

Table 1-1. Lista programas

ProgramaVersionTemaUbicaciónModule
Abricate 0.9.8Mass screening of contigs for antimicrobial resistance or virulence genes./share/apps/abricate-0.9.8programs/abricate-0.9.8
Abyss (compilado con MPI) 2.1.5Assemble large genomes using short reads./share/apps/Abyss-2.1.5-mpiprograms/abyss-2.1.5-mpi
AfterQC 0.9.7Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data./share/apps/AfterQC-0.9.7/programs/afterqc-0.9.7
Albacore 2.3.5The standard basecaller package for NanoPore.via conda..programs/albacore-2.3.5 (ver en programas especiales...)
Allpaths-LG 52488ALLPATHS-LG is a short-read assembler./share/apps/Allpaths-LG-52488/programs/allpaths
Amos 3.1.0-rc1AMOS is a collection of tools and class interfaces for the assembly of DNA reads./share/apps/Amos-3.1.0-rc1programs/amos-3.1.0-rc1
Antismash 4.1.0Search a genome sequence for secondary metabolite biosynthesis gene clusters.Modulo de Biocondaprograms/antismash-4.1.0
" " " 7.0.1 " " " Modulo de Biocondaprograms/antismash-7.0.1
Anvio 7.1an advanced analysis and visualization platform for omics dataModulo de Condaprograms/anvio-7.1
Anvio 8.0an advanced analysis and visualization platform for omics dataModulo de Condaprograms/anvio-8.0
Aragorn 2.41a program to detect tRNA genes and tmRNA genes in nucleotide sequence./share/apps/Aragorn-2.41programs/aragorn-2.41
aria2 1.36.0a lightweight multi-protocol & multi-source command-line download utility./share/apps/aria2-1.36.0programs/aria2-1.36.0
Art 2.5.8ART is a set of simulation tools to generate synthetic next-generation sequencing reads./share/apps/Art-2.5.8/programs/art-2.5.8
ARTDeco sin versiona pipeline for analyzing and characterizing transcriptional readthrough as described in Roth et al.paquage python 3programs/artdeco
Atlas 2.1.4Three commands to start analysing your metagenome data.Module Python3programs/atlas-2.1.4
Atropos 1.1.31a tool for specific, sensitive, and speedy trimming of NGS reads.Module Python3programs/atropos-1.1.31
Autocycler 0.2.1Autocycler is a tool for generating consensus long-read assemblies for bacterial genomes./share/apps/autocycler-0.2.1/programs/autocycler-0.2.1
Autodock 4.2.6AutoDock is a suite of automated docking tools./share/apps/autodock-4.2.6/programs/autodock-4.2.6
Autodock-Vina 1.1.2significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4../share/apps/autodock-vina-1.1.2/programs/autodock-vina-1.1.2
Bakta 1.9.2.rapid & standardized annotation of bacterial genomes, MAGs & plasmids.via conda programs/bakta-1.9.2
Bamtools 2.5.1BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files./share/apps/Bamtools-2.5.1/programs/bamtools-2.5.1
BaseSpace-Cli 1.5.4You can work with your BaseSpace Sequence Hub data using the command line interface (CLI)./share/apps/BaseSpace-Cli-1.5.4programs/basespace-cli-1.5.4
BayeScan 2.1Detecting natural selection from population-based genetic data./share/apps/BayeScan-2.1/programs/bayescan-2.1
BayesTraits 3.0.5a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available./share/apps/BayesTraits-3.0.5/programs/bayestraits-3.0.5
Basemount 0.15.96.2155BaseMount allows you to explore through runs, projects, samples, app results and analyses and interact directly with the associated files exactly as you would with any other file system.Instalado via rpm 
BBMap 38.26BBMap is a splice-aware global aligner for DNA and RNA sequencing reads./share/apps/BBMap-38.26/programs/bbmap-38.26
" 38.84 " /share/apps/BBMap-38.84/programs/bbmap-38.84
Beast2 2.4.5BEAST 2 is a cross-platform program for Bayesian MCMC analysis of molecular sequences./share/apps/Beats-2.4.5/programs/beast-2.4.5
Beast2 2.6.7BEAST 2 is a cross-platform program for Bayesian MCMC analysis of molecular sequences./share/apps/Beats-2.6.7/programs/beast-2.6.7
BEDops 2.4.40the fast, highly scalable and easily-parallelizable genome analysis toolkit/share/apps/Bedops-2.4.40/programs/bedops-2.4.40
Bcftools 1.9Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants./share/apps/bcftools-1.9/programs/bcftools-1.9
Bcftools 1.10.2Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants./share/apps/bcftools-1.10.2/programs/bcftools-1.10.2
Bcl2fastq 2.20To demultiplex data and convert BCL files to FASTQ file formats./share/apps/bcl2fastq-2.20/programs/bcl2fastq-2.20
Bedtools2 2.26.0The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage./share/apps/Bedtools2-2.26.0programs/bedtools2-2.26.0
Bedtools2 2.27.1The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage./share/apps/Bedtools2-2.27.1programs/bedtools2-2.27.1
Bellerophon sin versiona pipeline created to remove falsely assembled chimeric transcripts in de novo transcriptome assemblies.Package Condaprograms/bellerophon
bin3C 0.1.1bin3C : Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.Paquete Python 2programs/bin2c-0.1.1
BinSanity 0.2.7BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes.Paquete Python 2programs/binsanity-0.2.7
Bismark 0.23.1Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step./share/apps/Bismark-0.23.1/programs/bismark-0.23.1
Blast+ 2.7.1The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences./share/apps/Blast-2.7.1/programs/blast-2.7.1
" 2.9.0 " " "/share/apps/Blast-2.9.0/programs/blast-2.9.0
" 2.11.0 " " "/share/apps/Blast-2.11.0/programs/blast-2.11.0
" 2.12.0 " " "/share/apps/Blast-2.12.0/programs/blast-2.12.0
Blat 35BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm./share/apps/Blat-35/programs/blat-35
Bonito 0.3.1A PyTorch Basecaller for Oxford Nanopore Reads.Paquete python3programs/bonito-0.3.1
Bowtie1 1.2.3An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences./share/apps/Bowtie1-1.2.3/programs/bowtie1-1.2.3
Bowtie2 2.3.4.3An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences./share/apps/Bowtie2-2.3.4.3/programs/bowtie2-2.3.4.3
" " " 2.5.0 " " " /share/apps/Bowtie2-2.5.0/programs/bowtie2-2.5.0.
Bracken 2.5a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample./share/apps/Bracken-2.5/programs/bracken-2.5
Braker2 2.1.6an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.Package Condaprograms/braker2-2.1.6
BRB-seq 1.6BRB-seq tools suite was created in the early days of multiplexed libraries, when there was not many other alternatives to analyze BRB-seq libraries../share/apps/BRB-seq-1.6/programs/brb-seq-1.6
Busco 4.0.5BUSCO metric is complementary to technical metrics like N50Package Condaprograms/busco-4.0.5
" " " 5.3.2 " " " " " " programs/busco-5.3.2
" " " 5.4.7 " " " " " " programs/busco-5.4.7
Bwa 0.7.17An efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome./share/apps/Bwa-0.7.17programs/bwa-0.7.17
Canu 2.2A single molecule sequence assembler for genomes large and small./share/apps/Canu-2.2programs/canu-2.2
Casper 0.8.2(Context-Aware Scheme for Paired-End Read) is state-of-the art merging tool in terms of accuracy and robustness./share/apps/Casper-0.8.2programs/casper-0.8.2
CAT 4.6tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)./share/apps/CAT-4.6programs/cat-4.6
ccfind 1.4.5a general tool to detect circular complete genomes with clues of terminal redundancy./share/apps/ccfind-1.4.5programs/ccfind-1.4.5
Cd-hit 4.6.8A very widely used program for clustering and comparing protein or nucleotide sequences./share/apps/Cdhit-4.6.8programs/cdhit-4.6.8
Cd-hit 4.8.1A very widely used program for clustering and comparing protein or nucleotide sequences./share/apps/Cdhit-4.8.1programs/cdhit-4.8.1
cDNA_Cupcake 28.0a miscellaneous collection of Python and R scripts used for analyzing sequencing data.Paquage Condaprograms/cdna-cupcake-28.0
Cecret 3.7.20230620Cecret was originally developed by @erinyoung at the Utah Public Health Laborotory for SARS-COV-2./share/apps/Cecret-3.7.20230620/programs/cecret-3.7.20230620
Checkm2 1.0.1Rapid assessment of genome bin quality using machine learning..Ambiance condaprograms/checkm2-1.0.1
Circlator 1.5.5A tool to circularize genome assemblies.Paquete Python 3programs/circlator-1.5.5
ClonalFrameML 1.22A software package that performs efficient inference of recombination in bacterial genomes.Paquete Python 3programs/clonalframeml-1.12
CompareM 0.1.1a software toolkit which supports performing large-scale comparative genomic analyses.via condaprograms/comparem-0.1.1 (ver en programas especiales...)
cufflinks 2.2.1Transcriptome assembly and differential expression analysis for RNA-Seq./share/apps/Cufflinks-2.2.1programs/cufflinks-2.2.1
cutadapt 1.18Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.Paquete Python 3compilers/python-3.6.6
Deepbinner 0.2.0Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Paquete Python 3compilers/python-3.6.6
Deeploc (con licencia..) 2.Prediction of eukaryotic protein subcellular localization using deep learningPaquete condaprograms/deeploc-2
Deepsignal 0.1.8A deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads.Paquete condaprograms/deepsignal-0.1.8
DeepSimulator sin versionThe first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing./share/apps/DeepSimulator/programs/deepsimulator
DeepTools 3.1.2Tools for exploring deep sequencing data.Paquete Python compilers/python-3.6.6
Deepnano-blitz 0.1a very fast basecaseller which can basecall reads as fast as they come from MinION on ordinary laptop.Paquete condaprograms/deepnanoblitz-0.1
DeepVirFinder -- git release --predicts viral sequences using deep learning method..Paquete Python 3programs/deepvirfinder
Diamond 0.9.22A BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode)./share/apps/Diamond-0.9.22/programs/diamond-0.9.22
" " 2.0.4 " " /share/apps/Diamond-2.0.4programs/diamond-2.0.4
" " 2.1.8 " " /share/apps/Diamond-2.1.8programs/diamond-2.1.8
Discovar 52488Discovar is a Genome variant discovery through assembly./share/apps/Discovar-52488/programs/discovar-52488
Discovar de novo 52488Discovar de novo is a new genome assembler./share/apps/Discovardenovo-52488/programs/discovardenovo-52488
DRAM 1.1.1A tool for annotating metagenomic assembled genomes and VirSorter identified viral contigs.via condaprograms/dram-1.1.1
DWGSIM 0.1.13Whole Genome Simulator for Next-Generation Sequencing./share/apps/dwgsim-0.1.13programs/dwgsim-0.1.13
" " " 0.1.14 " " " /share/apps/dwgsim-0.1.14programs/dwgsim-0.1.14
Edirect ( NCBI Entrez Direct ) 11.3Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window./share/apps/edirect-11.3programs/edirect-11.3
eggNOG mapper 2.1.2a tool for fast functional annotation of novel sequences.Module Python3programs/eggnog-mapper-2.1.2
Eigensoft 7.2.1combines functionality from our population genetics methods and our EIGENSTRAT stratification correction method./share/apps/EIG-7.2.1/programs/eig-7.2.1
Emboss 6.6.0The European Molecular Biology Open Software Suite./share/apps/Emboss-6.6.0programs/emboss-6.6.0
Erne 2.1.1The Extended Randomized Numerical alignEr using BWT./share/apps/Erne-2programs/erne-2.1.1
Ete3 3.1.1A Python Environment for (phylogenetic) Tree Exploration.Paquete Python 3compilers/python-3.6.6
Exomiser 11.0.0The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data./share/apps/exomiser-cli-11.0.0programs/exomiser-cli-11.0.0
Exonerate 2.2.0Exonerate is a generic tool for pairwise sequence comparison./share/apps/exonerate-2.2.0programs/exonerate-2.2.0
" " " 2.4.0 " " " /share/apps/exonerate-2.4.0programs/exonerate-2.4.0
eXpress 1.5.1eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences./share/apps/express-1.5.1programs/express-1.5.1
FAPROTAX 1.2.4Functional Annotation of Prokaryotic Taxa./share/apps/FAPROTAX-1.2.4programs/faprotax-1.2.4
Fasta 36find regions of local or global similarity between Protein or DNA sequences./share/apps/Fasta-36programs/fasta-36
FastANI 1.1for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)./share/apps/FastANI-1.1/programs/fastani-1.1
" " " 1.33 " " " /share/apps/FastANI-1.33/programs/fastani-1.33
" " " 1.34 " " " /share/apps/FastANI-1.34/programs/fastani-1.34
Fastp 0.19.4An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)./share/apps/Fastp-0.19.4/programs/fastp-0.19.4
" 0.20.0 " /share/apps/Fastp-0.20.0/programs/fastp-0.20.0
FastQC 0.11.7A quality control tool for high throughput sequence data./share/apps/FastQC-0.11.7/programs/fastqc-0.11.7
" " " 0.12.1 " " " /share/apps/FastQC-0.12.1/programs/fastqc-0.12.1
FastTree 2.1.10FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences./share/apps/FastTree-2.1.10/programs/fasttree-2.1.10
" " " 2.1.11 " " " /share/apps/FastTree-2.1.11/programs/fasttree-2.1.11
FastViromeExplorer ..master.. de gitIndentify the viruses/phages and their abundance in the viral metagenomics data./share/apps/FastViromeExplorer/programs/fastviromeexplorer
Fastx-Toolkit 0.13.0a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing./share/apps/Fastx-Toolkit-0.13.0programs/fastx-toolkit-0.13.0
FCS adaptor 0.5.4FCS-adaptor detects adaptor and vector contamination in genome sequences./share/apps/fcs-adaptor-0.5.4/programs/fcs-adaptor-0.5.4
FCS-GX 0.5.4FCS-GX detects contamination from foreign organisms in genome sequences./share/apps/fcs-gx-0.5.4/programs/fcs-gx-0.5.4
Filtlong 0.2.0Filtlong is a tool for filtering long reads by quality./share/apps/Filtlong-0.2.0/programs/filtlong-0.2.0
FindFungi 0.23.3A pipeline for the identification of fungi in public metagenomics datasets./share/apps/FindFungi-0.23.3/programs/findfunfi-0.23.3
Flappie 1.1.0Flip-flop basecaller for Oxford Nanopore reads./share/apps/Flappie-1.1.0programs/flappie-1.1.0
Flye 2.6De novo assembler for single molecule sequencing reads using repeat graphs./share/apps/Flye-2.6programs/flye-2.6
" " " 2.9 " " " /share/apps/Flye-2.9programs/flye-2.9
fqtrim 0.9.7filtering and trimming next generation sequencing reads./share/apps/fqtrim-0.9.7programs/fqtrim-0.9.7
Flash 1.2.11FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments./share/apps/Flash-1.2.11programs/flash-1.2.11
Focus 1.8.0FOCUS: An Agile Profiler for Metagenomic Datapaquete Python 3programs/focus-1.8.0
FragGeneScan 1.31an application for finding (fragmented) genes in short reads./share/apps/FragGeneScan/programs/fraggenescan-1.31
Freebayes 1.2.0Bayesian haplotype-based polymorphism discovery./share/apps/Freebayes-1.2.0/programs/freebayes-1.2.0
" " " 1.3.6 " " " /share/apps/Freebayes-1.3.6/programs/freebayes-1.3.6
Fustr sin versiona pipeline that clusters coding sequences from transcriptomes into protein families./share/apps/FUSTrprograms/fustr (ver en programas especial)
GapFiller 2.1.1A seed-and-extend local assembler to fill the gap within paired reads./share/apps/Gapfiller-2.1.1/programs/gapfiller-2.1.1
GATK 4.1.4.1Variant Discovery in High-Throughput Sequencing Data./share/apps/gatk-4.1.4.1programs/gatk-4.1.4.1
" " " 4.6.0.0 " " " /share/apps/gatk-4.6.0.0programs/gatk-4.6.0.0
GeneMark-ES 1A family of gene prediction programs (Bajo licencia!)/share/apps/GeneMark-ESprograms/genemark-es
genoMad 1.8.0a tool that identifies virus and plasmid genomes from nucleotide sequences./share/apps/genomad-1.8.0/programs/genomad-1.8.0
UCSC Genome Browser Utilities s/nAlgunas herramientas : bigWigMerge faToTwoBit twoBitInfo twoBitToFa ./share/apps/UCSC_Utilitiesprograms/ucsc_utilities
Genomemapper 0.4.4GenomeMapper is a short read mapping tool designed for accurate read alignments./share/apps/GenomeMapper-0.4.4programs/genomemapper-0.4.4
get_homologues 3.2a versatile software package for pan-genome analysis./share/apps/get_homologues-3.2programs/get_homologues-3.2
get_phylomarkers 1.2.9A pipeline to select optimal markers for microbial phylogenomics, population genetics and genomic taxonomy./share/apps/get_phylomarkers-1.2.9programs/get_phylomarkers-1.2.9
get_phylomarkers 2.2.9.1A pipeline to select optimal markers for microbial phylogenomics, population genetics and genomic taxonomy./share/apps/get_phylomarkers-2.2.9.1programs/get_phylomarkers-2.2.9.1
Gffcompare 0.10.6Classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF./share/apps/Gffcompare-0.10.6/programs/gffcompare-0.10.6
Glimer 3.02A system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses./share/apps/Glimmer-3.02/programs/glimmer-3.02
GlimerHMM 3.0.4A new gene finder based on a Generalized Hidden Markov Model (GHMM)./share/apps/GlimmerHMM-3.0.4/programs/glimmerhmm-3.0.4
Grinder 0.5.4Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms./share/apps/Grinder-0.5.4/compilers/perl-5.28
GraftM 0.13.1GraftM : a tool for finding genes of interest in metagenomes, metatranscriptomes, and whole genomes.paquete Python 3programs/graftm-0.13.1
GraftM 0.14.0GraftM : a tool for finding genes of interest in metagenomes, metatranscriptomes, and whole genomes./share/apps/graftM-0.14.0 y ambiente conda...programs/graftm-0.14.0
Graphlan 1.1.3GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees./share/apps/graphlan-1.1.3compilers/graphlan-1.1.3
Gromacs 2020.3Molecular dynamics software package mainly designed for simulations of proteins, lipids and nucleic acids./share/apps/Gromacs-2020.3/programs/gromacs-2020.3
" " 2024.5 " " /share/apps/Gromacs-2024.5/programs/gromacs-2024.5
" " 2025.0 " " /share/apps/Gromacs-2025.0/programs/gromacs-2025.0
GTDB-Tk 2.1.0a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.Module Python 3.9programs/gtdbtk-2.1.0
" " " 2.4.0 " " " Module Python 3.6programs/gtdbtk-2.4.0
GToTree 1.4.2User-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees..via conda..programs/gtotree-1.4.2
Guppy 6.5.7 " " /share/apps/ont-guppy-cpu-6.5.7/programs/guppy-6.5.7
HiCExplorer 3.7.2Set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data. Atencion: La version instalada es via un contenedor Singulariy, verificar la documentacion del mudule!!!/share/apps/HicExplorer-3.7.2/programs/hicexplorer-3.7.2
HiC-PRO 3.0.0An optimized and flexible pipeline for Hi-C data processing./share/apps/HiC-Pro_3.0.0programs/hic-pro-3.0.0
Hisat2 2.1.0Graph-based alignment of next generation sequencing reads to a population of genomes./share/apps/Hisat2-2.1.0programs/hisat2-2.1.0
Hmmer v2 2.3.2Profile hidden Markov models for biological sequence analysis./share/apps/Hmmer-2.3.2/ 
Hmmer v3 3.2.1Profile hidden Markov models for biological sequence analysis./share/apps/Hmmer-3.2.1/programs/hmmer-3.2.1
Hmmer v3 3.3.2Profile hidden Markov models for biological sequence analysis./share/apps/Hmmer-3.3.2/programs/hmmer-3.3.2
Homer 4.10Motif discovery and next generation sequencing analysis/share/apps/Homer-4.10/programs/homer-4.10
Humann 3.0.0a4next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.Ambiante condaprograms/humann-3.0.0
IQ-Tree 1.6.12Efficient software for phylogenomic inference./share/apps/iqtree-1.6.12/programs/iqtree-1.6.12
iVar 1.0A computational package that contains functions broadly useful for viral amplicon-based sequencing./share/apps/ivar-1.0/programs/ivar-1.0
" " 1.3.1" " " /share/apps/ivar-1.3.1/programs/ivar-1.3.1
Idba 1.1.3a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth./share/apps/Idba-1.1.3/programs/idba-1.1.3
Idba-mt 1.0is a post-processing software for IDBA-UD contigs for removing chimeria contigs and extending contig length using paired-end reads information./share/apps/Idba-MT-1.0programs/idba-mt-1.0
Infernal 1.1.3for searching DNA sequence databases for RNA structure and sequence similarities./share/apps/infernal-1.1.3/programs/infernal-1.1.3
Interproscan 5.51-85.0a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains../share/apps/interproscan-5.51-85.0programs/interproscan-5.51-85.0
" " " 5.55-88.0 " " " /share/apps/interproscan-5.51-88.0programs/interproscan-5.55-88.0
" " " 5.73-104.0 " " " /share/apps/interproscan-5.73-104.0programs/interproscan-5.73-104.0
Ipyrad 0.9.99an interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types.Package Condaprograms/ipyrad-0.9.99
ITSxpress 2.0.0Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis.Package Condaprograms/itsxpress-2.0.0
Jellyfish 2.2.10A fast multi-threaded k-mer counter/share/apps/jellyfish-2.2.10/programs/jellyfish-2.2.10
jModelTest 2.1.10a tool to carry out statistical selection of best-fit models of nucleotide substitution./share/apps/jModelTest-2-1.10/programs/jmodeltest-2.1.10
Kaiju 1.7.3a program for the taxonomic classification of high-throughput sequencing reads./share/apps/kaiju-1.7.3/programs/kaiju-1.7.3
" " 1.8.0 " " /share/apps/kaiju-1.8.0/programs/kaiju-1.8.0
Kallisto 0.44.0a program for quantifying abundances of transcripts from RNA-Seq data./share/apps/Kallisto-0.44.0/programs/kallisto-0.44.0
Kraken 2 2.1.3a taxonomic sequence classifier./share/apps/Kraken-2.1.3/programs/kraken-2.1.3
" " " 2.1.4 " " " /share/apps/Kraken2-2.1.4/programs/kraken2-2.1.4
Kraken-biom 1.0.1Create BIOM-format tables from Kraken output.Module python 3programs/kraken-biom-1.0.1
LongQC 1.2.0c.a tool for the data quality control of the PacBio and ONT long reads, and it has two functionalities: sample qc and platform qc./share/apps/LongQC-1.2.0cprograms/longqc-1.2.0c
Macs 3.0.0a6Model-based Analysis for ChIP-SeqModule python 3programs/macs-3.0.0a6
Mafft 7.407Multiple alignment program for amino acid or nucleotide sequences/share/apps/Mafft-7.407programs/mafft-7.407
" " " 7.505 " " " /share/apps/Mafft-7.505programs/mafft-7.505
Manorm ??A robust model for quantitative comparison of ChIP-Seq data sets./share/apps/MAnormprograms/manorm
Mauve 2015-02-13Multiple Alignment of Conserved Genomic Sequence with Rearrangements./share/apps/mauve-2015-02-13programs/mauve-2015-02-13
MASH 2.3Fast genome and metagenome distance estimation using MinHash./share/apps/Mash-2.3programs/mash-2.3
Masurca 3.3.4The MaSuRCA (Maryland Super Read Cabog Assembler) assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches./share/apps/Masurca-3.3.4programs/masurca-3.3.4
Masurca 3.4.2 " " /share/apps/Masurca-3.4.2programs/masurca-3.4.2
MaxBin 2.2.7MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm./share/apps/MaxBin-2.2.7programs/maxbin-2.2.7
Medaka 0.11.5Sequence correction provided by ONT Research.Module Python3programs/medaka-0.11.5
Megahit 1.1.3An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph./share/apps/Megahit-1.1.1programs/megahit-1.1.3
Meme 4.11.3Perform motif discovery on DNA, RNA, protein or custom alphabet datasets./share/apps/Meme-4.11.3programs/meme-4.11.3
MetaBat 236d20e76303A robust statistical framework for reconstructing genomes from metagenomic data./share/apps/MetaBat-236d20e76303/programs/metabat-236d20e76303
MetaCluster 5.1a new software for binning short pair-end reads./share/apps/MetaCluster-5.1/programs/metacluster-5.1
MetaErg 1.2.3a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline./share/apps/Metaerg-1.2.3/programs/metaerg-1.2.3
Metaphlan v3 3.0.2Metagenomic Phylogenetic Analysis.Ambiente Condaprograms/metaphlan-3.0.2
Metaphlan v4 4.0.2Metagenomic Phylogenetic Analysis.Ambiente Condaprograms/metaphlan-4.0.2
Metascan 1.1an Metagenomic Scanning and Annotation tool, with an emphasis on metabolic genes.Ambiente Conda ligado con prokkaprograms/metasca-1.1
MetaVelvet-SL 1.0An extension of Velvet assembler to de novo metagenomic assembler utilizing supervised learning./share/apps/MetaVelvet-SL-1.0/programs/metavelvet-sl-1.0
MetaWrap 1.3aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish.Ambiente Condaprograms/metawrap-1.3
MetReTrim sin versiona pipeline, written in python, for trimming heterogeneity 'N' spacers from the pre-processed reads given the primer sequences./share/apps/MetReTrim/programs/metretrim
Minced 0.4.2a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as assembled contigs from metagenomes./share/apps/minced-0.4.2programs/minced-0.4.2
Miniasm 0.3-r179Ultrafast de novo assembly for long noisy reads (though having no consensus step)./share/apps/Miniasm-0.3-r179programs/miniasm-0.3-r179
Minimap2 2.14-r883A versatile pairwise aligner for genomic and spliced nucleotide sequences./share/apps/Minimap2-2.14-r883programs/minimap2-2.14-r883
" 2.17 " /share/apps/Minimap2-2.17programs/minimap2-2.17
MinPath 1.6a parsimony approach for biological pathway reconstructions using protein family predictions./share/apps/MinPath-1.6programs/minpath-1.6
Mira 4.0.2Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data./share/apps/mira-4.0.2programs/mira-4.0.2
miRanda 3.3aan algorithm for finding genomic targets for microRNAs.Module condaprograms/miranda-3.3a
Mirdeep2 0.1.3Discovering known and novel miRNAs from deep sequencing data./share/apps/mirdeep2-0.1.3programs/mirdeep2-0.1.3
MMseqs2 13-45111a software suite to search and cluster huge sequence sets./share/apps/MMseqs2-13-45111programs/mmseqs2-13-45111
" " " 14-7e284 " " " /share/apps/MMseqs2-14-7e284programs/mmseqs2-14-7e284i
" " " 17-b804f " " " /share/apps/MMseqs2-17-b804fprograms/mmseqs2-17-b804f
Mob-suite 3.1.8via conda./share/apps/Modeller-9.21programs/modeller-9.21
Modeller 9.21For homology or comparative modeling of protein three-dimensional structures (1,2)./share/apps/Modeller-9.21programs/modeller-9.21
Mosaik 2.2.30reference-guided aligner for next-generation sequencing technologies./share/apps/Mosaik-2.2.30programs/mosaik-2.2.30
MrBayes 3.2.6MrBayes is a program for Bayesian inference and model choice across a large space of phylogenetic and evolutionary models./share/apps/MrBayes-3.2.6programs/mrbayes-3.2.6
Multiqc 1.23a reporting tool that parses results and statistics from bioinformatics tool outputs, such as log files and console outputs.Module Pythonprograms/multiqc-123
Mummer 3.23Ultra-fast alignment of large-scale DNA and protein sequences./share/apps/Mummer-3.23programs/mummer-3.23
Muscle 3.8.1551Multiple sequence alignment. Faster and more accurate than CLUSTALW./share/apps/Muscle-3.8.1551programs/muscle-3.8.1551
MycobiomeScan 2.0Characterisation of fungal fraction in metagenomic surveys, with high end-user flexibility in terms of database creation and customisation./share/apps/MScan-2.0programs/mycobiomescan-2.0
Nanoplot 1.19.0Plotting tool for long read sequencing data and alignments.Paquete python 3compilers/python-3.6.6
Nanopolish 1.10.2Signal-level algorithms for MinION data /share/apps/Nanopolish-0.10.2programs/nanopolish-0.10.2
Nextalign 0.1.6Nextalign is a sequence reference alignment tool which uses the same alignment algorithm as Nextclade /share/apps/nextalign-0.1.6programs/nextalign-0.1.6
Nextalign 1.11.0Nextalign is a sequence reference alignment tool which uses the same alignment algorithm as Nextclade /share/apps/nextalign-1.11.0programs/nextalign-1.11.0
Nextclade 0.13.0Nextclade : Clade assignment, mutation calling, and sequence quality checksEn Node.jsprograms/nextxlade-0.13.0
Nextclade 1.11.0Nextclade : Clade assignment, mutation calling, and sequence quality checks/share/apps/nextclade-1.11.0programs/nextxlade-1.11.0
NGSutils 0.5.9NGSUtils : Tools for next-generation sequencing analysis.Ambiente Condaprograms/ngsutils-0.5.9
Nonpareil 3.4.1Nonpareil uses the redundancy of the reads in metagenomic datasets to estimate the average coverage and predict the amount of sequences that will be required to achieve nearly complete coverage.Ambiente Concaprograms/nonpareil-3.4.1
Nseg ? Low complexity sequence identification./share/apps/nsegprograms/nseg
Octave 3.8.2a high-level language, primarily intended for numerical computations.Instalado via RPM 
OpenRDP v0.1.0-rc2an open-source re-implementation of the RDP recombination detection program.Programa Pythonprograms/openrdp-v0.1.0-rc2
OrthoFinder 2.5.5a fast, accurate and comprehensive platform for comparative genomics./share/apps/OrthoFinder-2.5.5programs/orthofinder-2.5.5
Pandaseq 2.11a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence./share/apps/pandaseq-2.11programs/pandaseq-2.1
Paragraph 2.4aParagraph aims to facilitate this by providing an accurate genotyper for Structural Variations with short-read data./share/apps/Paragraph-2.4a/programs/paragraph-2.4a
Parallel-META 2.4.1Parallel-META is a a comprehensive and full-automatic computational toolkit for rapid data mining among metagenomic datasets./share/apps/parallel-meta-2.4.1/programs/parallel-meta-2.4.1
" " " 3.5.3 " " " /share/apps/parallel-meta-3.5.3/programs/parallel-meta-3.5.3
" " " 3.7.0 " " "/share/apps/parallel-meta-3.7-0/programs/parallel-meta-3.7.0
PATT 0.0.1Proteome Annotation Transfer Tool (pipeline de la UUSMB)./share/apps/PATTprograms/patt
pb-assembly 0.0.8.dentro de minicondaprograms/pb-assembl-0.0.8
pharokka 1.7.2a rapid standardised annotation tool for bacteriophage genomes and metagenomes.Ambiante condaprograms/pharokka-1.7.2
Picard 2.18.14A set of tools (in Java) for working with next generation sequencing data in the BAM format../share/apps/picard-tools-2.18.14programs/picard-2.18.14
Picrust2 2.3.0_ba software for predicting functional abundances based only on marker gene sequences.dentro de minicondaprograms/picrust2-2.3.0_b
Picrust2 (plugin qiime2) 2.3.0_ba software for predicting functional abundances based only on marker gene sequences.plugin qiime2programs/qiime2-2019.10
Pigz 2.4A parallel implementation of gzip for modern multi-processor, multi-core machines./share/apps/External/pigz-2.4programs/pigz-2.4
Pilon 1.23Automatically improve draft assemblies / Find variation among strains, including large event detection/share/apps/Pilon-1.23programs/pilon-1.23
" " " 1.24 " " " /share/apps/Pilon-1.24programs/pilon-1.24
Plass 5-cf8933Plass (Protein-Level ASSembler) and PenguiN (Protein guided nucleotide assembler) are software to assemble protein sequences or DNA/RNA contigs from short read sequencing data meant to work best for complex metagenomic or metatranscriptomic datasets./share/apps/plass-5-cf8933programs/plass-5-cf8933
Platanus 1.2.4PLATform for Assembling NUcleotide Sequences/share/apps/Platanus-1.2.4programs/platanus-1.2.4
Plink 1.9 free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner./share/apps/plink-1.9programs/plink-1.9
Pomoxis 0.2.3Pomoxis comprises a set of basic bioinformatic tools tailored to nanopore sequencing.dentro de minicondaprograms/pomoxis-0.2.3
Porechop 0.2.4Porechop is a tool for finding and removing adapters from Oxford Nanopore reads./share/apps/Porechop-0.2.4/programs/porechop-0.2.4
pplacer 1.1.alpha19Phylogenetic placement and downstream analysis./share/apps/pplacer-1.1.alpha19programs/pplacer-1.1.alpha19
Pratt 2.1A tool for finding flexible patterns in unaligned protein sequences./share/apps/Pratt-2.1programs/pratt-2.1
Preseq 2.0.1The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library/share/apps/preseq-2.0.1/programs/preseq-2.0.1
Prodigal 2.6.3Fast, reliable protein-coding gene prediction for prokaryotic genomes./share/apps/Prodigal-2.6.3programs/prodigal-2.6.3
Proteinortho 6.0.33a tool to detect orthologous genes within different species./share/apps/proteinortho-6.0.33programs/proteinortho-6.0.33
Protest3 3.4.2a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand./share/apps/prottest3-3.4.2programs/prottest3-3.4.2
Prokka 1.14.6rapid prokaryotic genome annotation./share/apps/prokka-1.14.6programs/prokka-1.14.6
pyEGA3 5.0.2The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets.paquete pythoncompilers/python-3.9.4
Qiime2 2019.4a next-generation microbiome bioinformatics platform.via conda..programs/qiime2-2019.4 (ver en programas especiales...)
" " " 2019.10a next-generation microbiome bioinformatics platform.via conda..programs/qiime2-2019.10 (ver en programas especiales...)
" " " 2022.8a next-generation microbiome bioinformatics platform.via conda..programs/qiime2-2022.8 (ver en programas especiales...)
" " " 2024.5a next-generation microbiome bioinformatics platform.via conda..programs/qiime2-2024.5 (ver en programas especiales...)
Quast (MetaQuast) 5.0.2 evaluates genome assemblies by computing various metrics. Paquete Python 3compilers/python-3.6.6
R Project 4.0.3 R is a free software environment for statistical computing and graphics./share/apps/R-4.0.3/programs/R-4.0.3
" " " 4.1.2 " " " /share/apps/R-4.1.2/programs/R-4.1.2
" " " 4.4.2 " " " /share/apps/R-4.4.2/programs/R-4.4.2
Racon 1.3.1Consensus module for raw de novo DNA assembly of long uncorrected reads./share/apps/Racon-1.3.1programs/racon-1.3.1
Randfold 2.0.1Minimum free energy of folding randomization test software./share/apps/Randfold-2.0.1programs/randfold-2.0.1
Ratatosk 0.2Hybrid error correction of long reads using colored de Bruijn graphs/share/apps/Ratatosk-0.2programs/ratatosk-0.2
RAxML 8.2.12Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. Utiliza 2 threads por defaults!/share/apps/RAxML-8.2.12programs/raxml-8.2.12
Rcorrector 1.0.4Efficient and accurate error correction for Illumina RNA-seq reads./share/apps/Rcorrector-1.0.4programs/rcorrector-1.0.4
Recon 1.08a package for automated de novo identification of repeat families from genomic sequences./share/apps/Recon-1.08programs/recon-1.08
RepeatMasker 4.0.8a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences./share/apps/RepeatMasker-4.0.8programs/repeatmasker-4.0.8
" " " 4.2.1 " " " /share/apps/RepeatMasker-4.2.1programs/repeatmasker-4.2.1
RepeatModeler 1.0.11a de novo repeat family identification and modeling package./share/apps/RepeatModeler-1.0.11programs/repeatmodeler-1.0.11
" " " 2.0.3 " " " /share/apps/RepeatModeler-2.0.3programs/repeatmodeler-2.0.3
RepeatScout 1.0.5identify repeat family sequences from genomes where hand-curated repeat databases (a la RepBase update) are not available./share/apps/RepeatSout-1.0.5programs/repeatscout-1.0.5
RMBlast 2.6.0RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program./share/apps/rmblast-2.6.0programs/rmblast-2.6.0
RNAhybrid 2.1.2RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA./share/apps/RNAhybrid-2.1.2programs/rnahybrid-2.1.2
Rnammer 1.2RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences./share/apps/rnammer-1.2programs/rnammer-1.2
Roary 3.13.0The pan genome pipeline.Ambiante condaprograms/roary-3.13.0
Rsem 1.3.1RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data./share/apps/Rsem-1.3.1programs/rsem-1.3.1
Salmon 0.11.3Salmon is a tool for wicked-fast transcript quantification from RNA-seq data./share/apps/Salmon-0.11.3/programs/salmon-0.11.3
" " " 1.10.3 " " " /share/apps/Salmon-1.10.3/programs/salmon-1.10.3
Samtools 0.1.18Flexible generic format for storing nucleotide sequence alignment/share/apps/samtools-0.1.18/programs/samtools-0.1.18
Samtools 1.9 " " " /share/apps/samtools-1.9/programs/samtools-1.9
Samtools 1.10 " " " /share/apps/samtools-1.10/programs/samtools-1.10
SCRMshaw_HD git versionGenome-wide CRM Prediction Program/share/apps/SCRMshaw_HD.git/programs/scrmshaw_hd-git
SEACR 1.4.beta2SEACR is intended to call peaks and enriched regions from sparse CUT and RUN or chromatin profiling data in which background is dominated by "zeroes" (i.e. regions with no read coverage)./share/apps/SEACR-1.4.b2/programs/seacr-1.4.b2
seq_scrumbs 0.1.9Little sequence file utilities meant to work within Unix pipelines Paquete Python2compilers/python-2.7.15
Seqkit 0.9.1A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang /share/apps/Seqkit-0.9.1programs/seqkit-0.9.1
" " 0.13.2 " " " /share/apps/Seqkit-0.13.2programs/seqkit-0.13.2
" " " 2.5.1 " " " /share/apps/Seqkit-2.5.1programs/seqkit-2.5.1
Shasta 0.5.1The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells./share/apps/shasta-0.5.1programs/shasta-0.5.1
Shore 0.9.3SHORE is a mapping and analysis pipeline for short DNA sequences./share/apps/Shore-0.9.3programs/shore-0.9.3
ShoreMap 3.6ShoreMap : For fast and accurate identification of causal mutations in plants./share/apps/ShoreMap-3.6programs/shoremap-3.6
Signalp (requiere licencia) 4.1SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms./share/apps/signalp-4.1programs/signalp-4.1
" " " 5.0b " " " " "/share/apps/signalp-5.0bprograms/signalp-5.0b
" " " 6.0g " " " " "Ambiente condaprograms/signalp-6.0g
Skani 0.2.2a program for calculating average nucleotide identity (ANI) and aligned fraction (AF) for DNA sequences (contigs/MAGs/genomes) and ANI./share/apps/skani-0.2.2/programs/skani-0.2.2
Skewer 0.2.2Implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences./share/apps/skewer-0.2.2/programs/skewer-0.2.2
Smalt 0.7.6A mapper for DNA sequencing reads./share/apps/Smalt-0.7.6programs/smalt-0.7.6
Snap 2.0.1Scalable Nucleotide Alignment Program./share/apps/snap-2.0.1programs/snap-2.0.1
Snakemake 5.3.0Aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment.Paquete Python 3compilers/snakemake-5.3.0
" 5.5.0""compilers/snakemake-5.5.0
" 5.10.0""compilers/snakemake-5.10.0
Snippy 4.6.0Snippy finds SNPs between a haploid reference genome and your NGS sequence reads/share/apps/snippy-4.6.0/compilers/snippy-4.6.0
snpEff 5.2eSnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes)./share/apps/snpEff-5.2eprograms/snpeff-5.2e
SortMeRNA 4.3.7a local sequence alignment tool for filtering, mapping and clustering.Paquete Condaprograms/sortmerna-4.3.7
Sourmash 3.0.1Compute and compare MinHash signatures for DNA data sets.Paquete Python3compilers/python-3.6.6
" " " 4.8.11Compute and compare MinHash signatures for DNA data sets.Paquete Python3programs/sourmash-4.8.11
spacegraphcats 1.2Explore large, annoying graphs using hierarchies of dominating sets./share/apps/spacegraphcatsprograms/spacegraphcats-1.2
SPAdes 3.15.4St. Petersburg genome assembler : is an assembly toolkit containing various assembly pipelines./share/apps/SPAdes-3.15.4programs/spades-3.15.4
" 4.0.0"/share/apps/SPAdes-4.0.0programs/spades-4.0.0
" 4.1.0"/share/apps/SPAdes-4.1.0programs/spades-4.1.0
SqueezeMeta 1.4.0A complete pipeline for metagenomic analysis./share/apps/SqueezeMeta-1.4.0programs/squeezemeta-1.4.0
" " " 1.5.2A complete pipeline for metagenomic analysis./share/apps/SqueezeMeta-1.5.2programs/squeezemeta-1.5.2
sra-tools 3.0.0The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives./share/apps/sra-tools-3.0.0programs/sra-tools-3.0.0
Stacks 2.62a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform./share/apps/stacks-2.62programs/stacks-2.62
" " " 2.66 " " " /share/apps/stacks-2.66programs/stacks-2.66
STAR 2.7.10aSpliced Transcripts Alignment to a Reference./share/apps/Star-2.7.10aprograms/star-2.7.10a
" " " 2.7.11a " " " /share/apps/Star-2.7.11aprograms/star-2.7.11a
Super-Focus 0.34A tool for agile functional analysis of shotgun metagenomic data.via condaprograms/superfocus-0.34 (ver en programas especiales...)
Tandem Repeats Finder (TRF) 4.09./share/apps/trf-4.09/programs/trf-4.09
Tassel 5.2.60Trait Analysis by aSSociation, Evolution and Linkage./share/apps/tassel-5.2.60programs/tassel-5.2.60
Tmhmm 2.0cPrediction of transmembrane helices in proteins./share/apps/tmhmm-2.0cprograms/tmhmm-2.0c
TransDecoder 5.3.0Find Coding Regions Within Transcripts. /share/apps/TransDecoder-5.3.0/programs/transdecoder-5.3.0
TransLig 1.3.an efficient de novo trascriptome assembler for RNA-Seq data./share/apps/Translig-1.3/programs/translig-1.3
Transrate 1.0.1Transrate is software for de-novo transcriptome assembly quality analysis../share/apps/transrate-1.0.1/programs/transrate-1.0.1
TrimGalore 0.6.7a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data./share/apps/TrimGalore-0.6.7programs/trimgalore-0..6.7
Trimmomatic 0.38Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters./share/apps/Trimmomatic-0.38/programs/trimmomatic-0.38
" " " 0.39 " " " /share/apps/Trimmomatic-0.39/programs/trimmomatic-0.39
Trinity 2.8.4RNA-Seq de novo transcriptome assembly. /share/apps/trinityrnaseq-2.8.4/programs/trinityrnaseq-2.8.4
" 2.9.1" /share/apps/trinityrnaseq-2.9.1/programs/trinityrnaseq-2.9.1
" 2.15.1" /share/apps/trinityrnaseq-2.15.1/programs/trinityrnaseq-2.15.1
Trinotate 3.1.1Transcriptome Functional Annotation and Analysis /share/apps/Trinotate-3.1.1/programs/trinotate-3.1.1
UMI-tools 1.1.4Tools for dealing with Unique Molecular Identifiers.Paquete Python 3programs/umi-tools-1.1.4
Unicycler 0.4.8an assembly pipeline for bacterial genomes.Paquete Python 3programs/unicycler-0.4.8
Variant Tools 3.0.2an integrated annotation and analysis package for next-generation sequencing data.Paquete Python 3programs/varianttools-3.0.2
Vcftools 0.1.16a program package designed for working with VCF file./share/apps/Vcftools-0.1.16programs/vcftools-0.1.16
vContact2 0.9.11a tool to perform guilt-by-contig-association classification of viral genomic sequence data.Paquete Python 3programs/vcontact2-0.9.11
Vep 112VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions."/share/apps/vep-112programs/vep-112
Verkko 1.3.1a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads.Paquete Condaprograms/verkko-1.3.1
VENAS sin versiona Viral genome Evolution Network Analysis System./share/apps/Venasprograms/venas
Velvet 1.2.10Sequence assembler for very short reads./share/apps/Velvet-1.2.10programs/velvet-1.2.10
Vibrant 1.2.1Virus Identification By iteRative ANnoTation./share/apps/Vibrant-1.2.1/programs/vibrant-1.2.1
ViennaRNA 2.4.13The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. /share/apps/ViennaRNA-2.4.13/programs/viennarna-2.4.13
VirSorter 1.0.5mining viral signal from microbial genomic dataEn conda. Leer la documentacion adjunta del module ( module help programs/virsorter-1.0.5 ) .programs/virsorter-1.0.5
Vsearch 2.13.4Versatile open-source tool for metagenomics./share/apps/Vsearch-2.13.4/programs/vsearch-2.13.4
Wub 0.3.0Tools and software library developed by the ONT Applications group.Paquete python 3compilers/python-3.6.6

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