gencore_variant_detection

Summary

Coming soon!

Software Packages

bamtools

Version: 2.4.0

Conda Channel: bioconda

Summary:

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

bcftools

Version: 1.3.1

Conda Channel: bioconda

Summary:

Tools for dealing with BCF and VCF files

bedtools

Version: 2.25.0

Conda Channel: bioconda

Summary:

A powerful toolset for genome arithmetic

bioconductor-biobase

Version: 2.32.0

Conda Channel: bioconda

Summary:

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

blast

Version: 2.2.31

Conda Channel: bioconda

Summary:

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

blat

Version: 35

Conda Channel: bioconda

Summary:

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

bowtie2

Version: 2.2.8

Conda Channel: bioconda

Summary:

Fast and sensitive read alignment

bwa

Version: 0.7.15

Conda Channel: bioconda

Summary:

The BWA read mapper.

Version: 2.2.1

Conda Channel: bioconda

Summary:

Transcriptome assembly and differential expression analysis for RNA-Seq.

discovar

Version: 52488

Conda Channel: bioconda

Summary:

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

discovardenovo

Version: 52488

Conda Channel: bioconda

Summary:

Suitable for de novo assembly of large and small genomes.

freebayes

Version: 1.0.2.29

Conda Channel: bioconda

Summary:

Bayesian haplotype-based polymorphism discovery and genotyping

gatk

Version: 3.5

Conda Channel: bioconda

Summary:

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

pear

Version: 0.9.6

Conda Channel: bioconda

Summary:

paired-end read merger

perl-app-cpanminus

Version: latest

Conda Channel: bioconda

Summary:

get, unpack, build and install modules from CPAN

perl-biox-workflow-plugin-filedetails

Version: 0.11

Conda Channel: bioconda

Summary:

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

perl-biox-workflow-plugin-fileexists

Version: 0.13

Conda Channel: bioconda

Summary:

a plugin to BioX::Workflow

perl-biox-workflow

Version: 1.10

Conda Channel: bioconda

Summary:

A very opinionated template based workflow writer.

perl-hpc-runner-command

Version: 3.1.1

Conda Channel: bioconda

Summary:

picard

Version: 2.5.0

Conda Channel: bioconda

Summary:

prinseq

Version: 0.20.4

Conda Channel: bioconda

Summary:

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

r-base

Version: 3.3.1

Conda Channel: r

Summary:

r-essentials

Version: latest

Conda Channel: r

Summary:

Some essential packages for working with R

samtools

Version: 1.3.1

Conda Channel: bioconda

Summary:

Tools for dealing with SAM, BAM and CRAM files

seqtk

Version: 1.2

Conda Channel: bioconda

Summary:

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

snpeff

Version: 4.3

Conda Channel: bioconda

Summary:

Genetic variant annotation and effect prediction toolbox

snpsift

Version: 4.3

Conda Channel: bioconda

Summary:

star

Version: 2.5.2a

Conda Channel: bioconda

Summary:

An RNA-seq read aligner.

tophat

Version: 2.1.0

Conda Channel: bioconda

Summary:

A spliced read mapper for RNA-Seq

vcflib

Version: 1.0.0_rc1

Conda Channel: bioconda

Summary:

Command-line tools for manipulating VCF files

vcftools

Version: 0.1.14

Conda Channel: bioconda

Summary:

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

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