SingularityRecipes

Various Singularity recipes I've used to generate bioinformatics containers

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