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bioinfocontainers's Introduction

SingularityRecipes

Various Singularity recipes I've used to generate bioinformatics containers

https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg

Obtaining a container

singularity pull shub://jlboat/BioinfoContainers:fastp   # or exchange fastp for any other container listed here

Container Recipes

BCL Processing Programs

  • Singularity.bcl2fastq

FASTQ Processing Programs

  • Singularity.fastp
  • Singularity.fastqc
  • Singularity.sabre
  • Singularity.trimmomatic

Read Aligners

  • Singularity.hisat2
  • Singularity.STAR
  • Singularity.bwa

Expression Quantification/Alternative Splicing

  • Singularity.stringtie
  • Singularity.hmmsplicer

Variant Callers/Analysis tools

  • Singularity.vcftools
  • Singularity.snpeff

Differential Expression

  • Singularity.limma-voom

Report Generation

  • Singularity.multiqc

Various Scripts/Aggregate Programs

  • Singularity.bioscripts
  • Singularity.conda
  • Singularity.deeptools

Genome Viewers

  • Singularity.IGB
  • Singularity.IGV

bioinfocontainers's People

Contributors

jlboat avatar

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