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
Cufflinks-patch
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
Cufflinks
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