cgwyx/biosoft repository overview

⁠docker-bio

Dockerfile repository for Bioinformatics

⁠Docker images

• Images on Docker Hub:
  • abra2⁠
  • alfred⁠
  • ascat⁠
  • bcftools⁠
  • bedops⁠
  • bedtools⁠
  • bioconda⁠
  • bowtie2⁠
  • bwa⁠
  • bwa-mem2⁠
  • cufflinks⁠
  • cnvnator⁠
  • cutadapt⁠
  • delly⁠
  • elprep⁠
  • fastq-dump⁠
  • fastqc⁠
  • fgbio⁠
  • freec⁠
  • gatk⁠
  • gencore⁠
  • gffread⁠
  • gridss⁠
  • goleft⁠
  • hisat2⁠
  • igv
  • igv-webapp⁠
  • jbrowse⁠
  • kallisto⁠
  • last⁠
  • lumpy⁠
  • macs2⁠
  • manta⁠
  • miso⁠
  • msisensor⁠
  • msisensor-pro⁠
  • multiqc⁠
  • nirvana⁠
  • oncotator
  • picard⁠
  • pindel
  • prinseq⁠
  • rsem⁠
  • sambamba⁠
  • samplot⁠
  • samtools⁠
  • seqkit⁠
  • sigprofiler⁠
  • smoove⁠
  • snpeff⁠
  • star⁠
  • strelka⁠
  • svtools⁠
  • trim_galore⁠
  • trimmomatic⁠
  • varscan⁠
  • vep⁠
• Images requiring a user build:
  • annovar
  • bcl2fastq
• Images outside this repository:
  • deepvariant⁠
  • deepvariant_gpu⁠

⁠References

• abra2
  • GitHub - mozack/abra2⁠
• alfred
  • GitHub - tobiasrausch/alfred⁠
  • www.gear-genomics.com - Alfred⁠
• annovar
  • annovar.openbioinformatics.org - ANNOVAR⁠
• ascat
  • GitHub - Crick-CancerGenomics/ascat⁠
  • The Francis Crick Institute - Allele-Specific Copy number Analysis of Tumours (ASCAT)⁠
• bcftools
  • samtools.github.io - Bcftools⁠
  • GitHub - samtools/bcftools⁠
• bcl2fastq
  • Illumina - bcl2fastq Conversion Software⁠
• bedops
  • bedops.readthedocs.io - BEDOPS⁠
  • GitHub - bedops/bedops⁠
• bedtools
  • bedtools.readthedocs.io - bedtools2⁠
  • GitHub - arq5x/bedtools2⁠
• bioconda
  • bioconda.github.io - Bioconda⁠
• bowtie2
  • bowtie-bio.sourceforge.net - Bowtie 2⁠
  • GitHub - BenLangmead/bowtie2⁠
• bwa
  • bio-bwa.sourceforge.net - Burrows-Wheeler Aligner⁠
  • GitHub - lh3/bwa⁠
• bwa
  • GitHub - bwa-mem2/bwa-mem2⁠
• canvas
  • GitHub - Illumina/canvas⁠
• cn.mops
  • Bioconductor - cn.mops⁠
• cnvnator
  • GitHub - abyzovlab/cnvnator⁠
• cufflinks
  • Trapnell Lab - Cufflinks⁠
  • GitHub - cole-trapnell-lab/cufflinks⁠
• cutadapt
  • cutadapt.readthedocs.io - cutadapt⁠
  • GitHub - marcelm/cutadapt⁠
• deepvariant
  • GitHub -google/deepvariant⁠
  • Google Cloud Platform - DeepVariant⁠
• delly
  • GitHub - dellytools/delly⁠
• elprep
  • GitHub - ExaScience/elprep⁠
• fastq-dump
  • NCBI - SRA Toolkit⁠
• fastqc
  • Babraham Bioinformatics - FastQC⁠
• fgbio
  • GitHub - fulcrumgenomics/fgbio⁠
  • fulcrumgenomics.github.io - fgbio⁠
• freec
  • boevalab.inf.ethz.ch - Control-FREEC⁠
  • GitHub - BoevaLab/FREEC⁠
• gatk
  • Broad Institute - Genome Analysis Toolkit⁠
  • GitHub - broadinstitute/gatk⁠
• gencore
  • GitHub - OpenGene/gencore⁠
• gffread
  • GitHub - gpertea/gffread⁠
• gridss
  • GitHub - PapenfussLab/gridss⁠
• goleft
  • GitHub - brentp/goleft⁠
• hisat2
  • Johns Hopkins University - HISAT2⁠
  • GitHub - infphilo/hisat2⁠
• igv:
  • Broad Institute - Integrative Genomics Viewer⁠
  • GitHub - igvteam/igv⁠
• igv-webapp:
  • Broad Institute - Integrative Genomics Viewer⁠
  • GitHub - igvteam/igv-webapp⁠
• jbrowse
  • jbrowse.org - The JBrowse Genome Browser⁠
  • GitHub - GMOD/jbrowse⁠
• kallisto
  • pachterlab.github.io - kallisto⁠
  • GitHub - pachterlab/kallisto⁠
• last
  • last.cbrc.jp - LAST⁠
• lumpy
  • GitHub - arq5x/lumpy-sv⁠
• macs2
  • X. Shirley Liu Lab - MACS⁠
  • GitHub - taoliu/MACS⁠
• manta
  • GitHub - Illumina/manta⁠
• miso
  • miso.readthedocs.io - MISO⁠
  • hollywood.mit.edu - MISO⁠
  • GitHub - yarden/MISO⁠
• msisensor
  • GitHub - ding-lab/msisensor⁠
• msisensor-pro
  • GitHub - xjtu-omics/msisensor-pro⁠
• multiqc
  • GitHub - ewels/MultiQC⁠
• nirvana
  • GitHub - Illumina/Nirvana⁠
• oncotator
  • Broad Institute - Oncotator⁠
  • GitHub - broadinstitute/oncotator⁠
• picard
  • broadinstitute.github.io - Picard⁠
  • GitHub - broadinstitute/picard⁠
• pindel
  • GitHub - genome/pindel⁠
• prinseq
  • prinseq.sourceforge.net - PRINSEQ⁠
• rsem
  • deweylab.github.io - RSEM (RNA-Seq by Expectation-Maximization)⁠
  • GitHub - deweylab/RSEM⁠
• sambamba
  • GitHub - biod/sambamba⁠
  • lomereiter.github.io - Sambamba⁠
• samplot
  • GitHub - ryanlayer/samplot⁠
• samtools
  • samtools.sourceforge.net - SAMtools⁠
  • GitHub - samtools/samtools⁠
• seqkit
  • bioinf.shenwei.me - SeqKit⁠
  • GitHub - shenwei356/seqkit⁠
• sigprofiler
  • COSMIC Mutational Signatures - SigProfiler Tools⁠
  • GitHub - AlexandrovLab/SigProfilerMatrixGenerator⁠
  • GitHub - AlexandrovLab/SigProfilerPlotting⁠
  • GitHub - AlexandrovLab/SigProfilerExtractor⁠
  • GitHub - AlexandrovLab/SigProfilerSimulator⁠
• smoove
  • GitHub - brentp/smoove⁠
• snpeff
  • snpeff.sourceforge.net - SnpEff⁠
• star
  • GitHub - alexdobin/STAR⁠
• strelka
  • GitHub - Illumina/strelka⁠
• svtools
  • GitHub - hall-lab/svtools⁠
• trim_galore
  • GitHub - FelixKrueger/TrimGalore⁠
  • Babraham Bioinformatics - Trim Galore⁠
• trimmomatic
  • usadellab.org - Trimmomatic⁠
  • GitHub - timflutre/trimmomatic⁠
• varscan
  • massgenomics.org - VarScan⁠
  • dkoboldt.github.io - VarScan⁠
  • GitHub - dkoboldt/varscan⁠
• vep
  • www.ensembl.org - Ensembl Variant Effect Predictor (VEP)⁠
  • GitHub - Ensembl/ensembl-vep⁠

⁠Dependencies

Some images use the following tools:

• print-github-tags
  • Tiny command to fetch repository tags or releases from GitHub
  • GitHub - dceoy/print-github-tags⁠
• clir
  • R package manager for command line interface
  • GitHub - dceoy/clir⁠
  • DockerHub - dceoy/clir⁠