Software

Abyss

Summary

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

Version: 1.9.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0

Augustus

Summary

AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.

Version: 3.2.2

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_metagenomics-1.0-0

Autoconf

Summary

Extensible M4 macros that produce shell scripts to configure software source code packages.

Version: latest

Conda Channel: conda-forge

HPC Modules

  • gencore_build-1.0-1

Automake

Summary

Tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.

Version: latest

Conda Channel: conda-forge

HPC Modules

  • gencore_build-1.0-1

Bamtools

Summary

C++ API & command-line toolkit for working with BAM data

Version: 2.4.0

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Bcftools

Summary

Tools for dealing with BCF and VCF files

Version: 1.3.1

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Bedtools

Summary

A powerful toolset for genome arithmetic

Version: 2.25.0

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Bioconductor-ballgown

Summary

Version: 2.2.0

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Bioconductor-biobase

Summary

Functions that are needed by many other packages or which replace R functions.

Version: 2.32.0

Conda Channel: bioconda

HPC Modules

  • gencore_variant_detection-1.0-1

Bioconductor-biobase

Summary

Functions that are needed by many other packages or which replace R functions.

Version: latest

Conda Channel: bioconda

HPC Modules

  • gencore_r-3.3.1-0

Bioconductor-biocgenerics

Summary

S4 generic functions needed by many Bioconductor packages.

Version: latest

Conda Channel: bioconda

HPC Modules

  • gencore_base-1.0-1

Bioconductor-biovizbase

Summary

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

Version: 1.18.0

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Bioconductor-cummerbund

Summary

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

Version: 2.12.1

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq_malaria-1.0-0

Bioconductor-cummerbund

Summary

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

Version: 2.16.0

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Bioconductor-dada2

Summary

Exact sample inference from Illumina amplicon data. Resolves real variants differing by as little as one nucleotide.

Version: 1.0.3

Conda Channel: bioconda

HPC Modules

  • gencore_metagenomics-1.0-0

Bioconductor-deseq2

Summary

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

Version: 1.10.1

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq_malaria-1.0-0

Bioconductor-deseq2

Summary

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

Version: 1.12.4

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Bioconductor-deseq

Summary

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution

Version: 1.22.1

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq_malaria-1.0-0

Bioconductor-edger

Summary

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

Version: 3.14.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0

Bioconductor-genomicranges

Summary

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing data (a.k.a. NGS data). The package defines general purpose containers for storing genomic intervals. Specialized containers for representing and manipulating short alignments against a reference genome are defined in the GenomicAlignments package.

Version: 1.26.1

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Bioconductor-gviz

Summary

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Version: 1.16.5

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Bioconductor-s4vectors

Summary

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Version: 0.12.0

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Blast

Summary

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit.

Version: 2.2.31

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_variant_detection-1.0-1

Blat

Summary

BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.

Version: 35

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Bowtie2

Summary

Fast and sensitive read alignment

Version: 2.2.8

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Bwa

Summary

The BWA read mapper.

Version: 0.7.15

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_variant_detection-1.0-1

Cd-hit

Summary

Clusters and compares protein or nucleotide sequences

Version: 4.6.4

Conda Channel: bioconda

HPC Modules

  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0

Circos

Summary

Circos is a software package for visualizing data and information. It visualizes data in a circular layout

Version: 0.69.2

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0

Cmake

Summary

CMake is an extensible, open-source system that manages the build process

Version: 3.7.1

Conda Channel: conda-forge

HPC Modules

  • gencore_build-1.0-1

Summary

Transcriptome assembly and differential expression analysis for RNA-Seq

Version: 2.2.1

Conda Channel: nyuad-cgsb

HPC Modules

  • gencore_rnaseq-1.0-0

Summary

Transcriptome assembly and differential expression analysis for RNA-Seq.

Version: 2.2.1

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Ddocent

Summary

dDocent is an interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD data

Version: 2.1

Conda Channel: bioconda

HPC Modules

  • gencore_rad_ddocent-1.0-0

Deeptools

Summary

A set of user-friendly tools for normalization and visualzation of deep-sequencing data

Version: 2.3.2

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0

Discovar

Summary

Suitable for variant calling with reference and de novo assembly of small genomes.

Version: 52488

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_variant_detection-1.0-1

Discovardenovo

Summary

Suitable for de novo assembly of large and small genomes.

Version: 52488

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_variant_detection-1.0-1

Fastqc

Summary

A quality control tool for high throughput sequence data.

Version: 0.11.5

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0
  • gencore_rnaseq-1.0-0

Fastx_toolkit

Summary

Version: 0.0.14

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0

Freebayes

Summary

Bayesian haplotype-based polymorphism discovery and genotyping

Version: 1.0.2.29

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_rad-1.0-0
  • gencore_variant_detection-1.0-1

Gatk

Summary

The full Genome Analysis Toolkit (GATK) framework, license restricted.

Version: 3.5

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Gatk

Summary

The full Genome Analysis Toolkit (GATK) framework, license restricted.

Version: 3.6

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_rnaseq-1.0-0

Gcc

Summary

Version: latest

Conda Channel: default

HPC Modules

  • gencore_build-1.0-1

Genblasta

Summary

genBlast is a program suite, consisting of two programs: genBlastA and genBlastG. genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.

Version: 1.0.4

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0

Genblastg

Summary

genBlast is a program suite, consisting of two programs: genBlastA and genBlastG. genBlastA parses local alignments, or high-scoring segment pairs (HSPs) produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.

Version: 1.38

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0

Hisat2

Summary

graph-based alignment of next generation sequencing reads to a population of genomes

Version: 2.0.4

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Hmmer

Summary

Biosequence analysis using profile hidden Markov models

Version: 3.1b2

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_metagenomics-1.0-0

Htseq

Summary

A framework to process and analyze data from high-throughput sequencing (HTS) assays

Version: 0.6.1.post1

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0

Idba

Summary

IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

Version: 1.1.1

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0

Ipython

Summary

IPython: Productive Interactive Computing

Version: latest

Conda Channel: conda-forge

HPC Modules

  • gencore_python-1.0-0

Jellyfish

Summary

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence

Version: 2.2.3

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0

Kallisto

Summary

Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

Version: 0.43.0

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0

Kat

Summary

KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts

Version: 2.0.8

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1

Kmergenie

Summary

KmerGenie estimates the best k-mer length for genome de novo assembly

Version: 1.7016

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0

Kraken

Summary

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Version: 0.10.6_eaf8fb68

Conda Channel: bioconda

HPC Modules

  • gencore_kraken-1.0-0

Libgcc

Summary

Version: latest

Conda Channel: default

HPC Modules

  • gencore_build-1.0-1

M4

Summary

Version: latest

Conda Channel: bioconda

HPC Modules

  • gencore_build-1.0-1

Macs2

Summary

MACS -- Model-based Analysis of ChIP-Seq

Version: 2.1.1.20160309

Conda Channel: bioconda

HPC Modules

  • gencore_epigenetics-1.0-0

Mafft

Summary

Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform

Version: 7.221

Conda Channel: bioconda

HPC Modules

  • gencore_evonet-1.0-0

Mawk

Summary

mawk is an interpreter for the AWK Programming Language.

Version: 1.3.4

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_metagenomic-1.0-0
  • gencore_metagenomics-1.0-0

Mcl

Summary

MCL - a cluster algorithm for graphs

Version: 14.137

Conda Channel: bioconda

HPC Modules

  • gencore_evonet-1.0-0

Metaphlan2

Summary

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0 MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.

Version: 2.5.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_metagenomic-1.0-0

Metavelvet-sl-feature-extraction

Summary

Perl libraries that do feature extraction for metavelvet-sl

Version: 1.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_metagenomic-1.0-0

Metavelvet-sl

Summary

MetaVelvet-SL : An extension of Velvet assembler to de novo metagenomic assembler utilizing supervised learning

Version: 1.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_metagenomic-1.0-0

Metavelvet

Summary

MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Version: 1.1.01

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_metagenomic-1.0-0

Mira

Summary

MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)

Version: 4.0.2

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0

Mothur

Summary

Version: 1.36.1

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_metagenomic-1.0-0
  • gencore_metagenomics-1.0-0

Multiqc

Summary

Create aggregate bioinformatics analysis report across many samples

Version: 0.8

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0

Numpy

Summary

array processing for numbers, strings, records, and objects.

Version: 1.11.1

Conda Channel: conda-forge

HPC Modules

  • gencore_epigenetics-1.0-0

Numpy

Summary

array processing for numbers, strings, records, and objects.

Version: latest

Conda Channel: conda-forge

HPC Modules

  • gencore_python-1.0-0

Pauda

Summary

Version: 1.0.1

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1

Pear

Summary

paired-end read merger

Version: 0.9.6

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_variant_detection-1.0-1

Perl-app-cpanminus

Summary

get, unpack, build and install modules from CPAN

Version: latest

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_base-1.0-1
  • gencore_build-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_kraken-1.0-0
  • gencore_perl-1.0-0
  • gencore_variant_detection-1.0-1

Perl-biox-workflow-plugin-filedetails

Summary

Get metadata for files in directories processed by BioX::Workflow

Version: 0.11

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_base-1.0-1
  • gencore_build-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_genomic_soapdenovo2-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_evonet-1.0-0
  • gencore_kraken-1.0-0
  • gencore_perl-1.0-0
  • gencore_qc-1.0-0
  • gencore_rad-1.0-0
  • gencore_rad_ddocent-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_trinity-1.0-0
  • gencore_variant_detection-1.0-1

Perl-biox-workflow-plugin-fileexists

Summary

a plugin to BioX::Workflow

Version: 0.13

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_base-1.0-1
  • gencore_build-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_genomic_soapdenovo2-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_evonet-1.0-0
  • gencore_kraken-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_perl-1.0-0
  • gencore_qc-1.0-0
  • gencore_qiime-1.0-0
  • gencore_rad-1.0-0
  • gencore_rad_ddocent-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_trinity-1.0-0
  • gencore_variant_detection-1.0-1

Perl-biox-workflow

Summary

A very opinionated template based workflow writer.

Version: 1.10

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_base-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_genomic_soapdenovo2-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_evonet-1.0-0
  • gencore_kraken-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_perl-1.0-0
  • gencore_qc-1.0-0
  • gencore_qiime-1.0-0
  • gencore_rad-1.0-0
  • gencore_rad_ddocent-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_trinity-1.0-0
  • gencore_variant_detection-1.0-1

Perl-dbi

Summary

Database independent interface for Perl

Version: latest

Conda Channel: bioconda

HPC Modules

  • gencore_perl-1.0-0

Perl-hpc-runner-command

Summary

Version: 3.1.1

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_base-1.0-1
  • gencore_build-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_genomic_soapdenovo2-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_evonet-1.0-0
  • gencore_kraken-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_perl-1.0-0
  • gencore_qc-1.0-0
  • gencore_qiime-1.0-0
  • gencore_r-3.3.1-0
  • gencore_rad-1.0-0
  • gencore_rad_ddocent-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_trinity-1.0-0
  • gencore_variant_detection-1.0-1

Perl-termreadkey

Summary

A perl module for simple terminal control

Version: latest

Conda Channel: bioconda

HPC Modules

  • gencore_perl-1.0-0

Picard

Summary

Version: 2.0.1

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq_malaria-1.0-0

Picard

Summary

Version: 2.5.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_variant_detection-1.0-1

Prinseq

Summary

PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data

Version: 0.20.4

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Pyfaidx

Summary

pyfaidx: efficient pythonic random access to fasta subsequences

Version: 0.4.7.1

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0

Pyfasta

Summary

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

Version: 0.5.2

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0

Pyfastaq

Summary

Script to manipulate FASTA and FASTQ files, plus API for developers

Version: 3.11.0

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0

Python

Summary

General purpose programming language

Version: 2.7

Conda Channel: conda-forge

HPC Modules

  • gencore_epigenetics-1.0-0

Python

Summary

General purpose programming language

Version: 3.5

Conda Channel: conda-forge

HPC Modules

  • gencore_qc-1.0-0

Python

Summary

General purpose programming language

Version: latest

Conda Channel: conda-forge

HPC Modules

  • gencore_python-1.0-0

Qiime

Summary

Quantitative Insights Into Microbial Ecology

Version: 1.9.1

Conda Channel: bioconda

HPC Modules

  • gencore_qiime-1.0-0

Qualimap

Summary

Quality control of alignment sequencing data and its derivatives like feature counts

Version: 2.2.2a

Conda Channel: bioconda

HPC Modules

  • gencore_qc-1.0-0

Quast

Summary

Quality Assessment Tool for Genome Assemblies

Version: 4.1

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0

R-base

Summary

Version: 3.3.1

Conda Channel: r

HPC Modules

  • gencore_base-1.0-1
  • gencore_r-3.3.1-0
  • gencore_rnaseq-1.0-0
  • gencore_variant_detection-1.0-1

R-cairo

Summary

This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.

Version: latest

Conda Channel: r

HPC Modules

  • gencore_rnaseq-1.0-0

R-essentials

Summary

Some essential packages for working with R

Version: latest

Conda Channel: r

HPC Modules

  • gencore_r-3.3.1-0
  • gencore_rnaseq-1.0-0
  • gencore_variant_detection-1.0-1

R-ggplot2

Summary

An implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes. See http://ggplot2.org for more information, documentation and examples.

Version: latest

Conda Channel: bioconda

HPC Modules

  • gencore_base-1.0-1

R

Summary

Version: 3.3.1

Conda Channel: r

HPC Modules

  • gencore_r-3.3.1-0

Rainbow

Summary

Efficient tool for clustering and assembling short reads, especially for RAD

Version: 2.0.4

Conda Channel: bioconda

HPC Modules

  • gencore_rad-1.0-0

Repeatmasker

Summary

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

Version: 4.0.6

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1

Rmblast

Summary

RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.

Version: 2.2.28

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1

Rsem

Summary

RSEM (RNA-Seq by Expectation-Maximization)

Version: 1.2.28

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0
  • gencore_trinity-1.0-0

Salmon

Summary

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

Version: 0.6.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0

Samtools

Summary

Tools for dealing with SAM, BAM and CRAM files

Version: 1.3.1

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Scipy

Summary

Scientific Library for Python

Version: latest

Conda Channel: conda-forge

HPC Modules

  • gencore_python-1.0-0

Seqtk

Summary

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format

Version: 1.2

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Sickle

Summary

A lightweight OAI client library for Python

Version: 0.5

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0

Snpeff

Summary

Genetic variant annotation and effect prediction toolbox

Version: 4.3

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_variant_detection-1.0-1

Snpsift

Summary

Version: 4.3

Conda Channel: bioconda

HPC Modules

  • gencore_variant_detection-1.0-1

Soapdenovo2-gapcloser

Summary

a tool named GapCloser for SOAPdenovo.

Version: 1.12

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic_soapdenovo2-1.0-0

Soapdenovo2-prepare

Summary

SoapDenovo2 Data prepare module using assembled contig to do scaffold assembly

Version: 2.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic_soapdenovo2-1.0-0

Soapdenovo2

Summary

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.

Version: 2.40

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic_soapdenovo2-1.0-0

Spades

Summary

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.

Version: 3.9.0

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0

Stacks

Summary

Stacks is a software pipeline for building loci from RAD-seq

Version: 1.40

Conda Channel: bioconda

HPC Modules

  • gencore_rad-1.0-0

Star

Summary

An RNA-seq read aligner.

Version: 2.5.2a

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Stringtie

Summary

Transcriptome assembly and quantification for RNA-seq

Version: 1.3.0

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq-1.0-0

Tophat

Summary

A spliced read mapper for RNA-Seq

Version: 2.1.0

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Transdecoder

Summary

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

Version: 2.1.0

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_trinity-1.0-0

Trimmomatic

Summary

Genetic variant annotation and effect prediction toolbox

Version: 0.35

Conda Channel: bioconda

HPC Modules

  • gencore_rnaseq_malaria-1.0-0

Trimmomatic

Summary

Genetic variant annotation and effect prediction toolbox

Version: 0.36

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_qc-1.0-0
  • gencore_rnaseq-1.0-0

Trinity

Summary

Trinity assembles transcript sequences from Illumina RNA-Seq data

Version: 2.2.0

Conda Channel: bioconda

HPC Modules

  • gencore_trinity-1.0-0

Trinotate

Summary

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms

Version: 3.0.1

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_trinity-1.0-0

Vcflib

Summary

Command-line tools for manipulating VCF files

Version: 1.0.0_rc1

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Vcftools

Summary

A set of tools written in Perl and C++ for working with VCF files.

Version: 0.1.14

Conda Channel: bioconda

HPC Modules

  • gencore_annotation-1.0-1
  • gencore_de_novo_genomic-1.0-0
  • gencore_de_novo_metagenomic-1.0-0
  • gencore_de_novo_transcriptome-1.0-0
  • gencore_epigenetics-1.0-0
  • gencore_metagenomics-1.0-0
  • gencore_rad-1.0-0
  • gencore_rnaseq-1.0-0
  • gencore_rnaseq_malaria-1.0-0
  • gencore_variant_detection-1.0-1

Velvet

Summary

Sequence Assembler for short reads

Version: 1.2.10

Conda Channel: bioconda

HPC Modules

  • gencore_de_novo_genomic-1.0-0

Zlib

Summary

Massively spiffy yet delicately unobtrusive compression library

Version: latest

Conda Channel: conda-forge

HPC Modules

  • gencore_build-1.0-1

results matching ""

    No results matching ""