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.
cufflinks
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.