zlskidmore

HTSeq sequencing data analysis and read counting, with htseq-qa support.

rMATS-turbo for differential alternative splicing analysis, with STAR and samtools.

Extract mutation signatures

Docker image for R available here: https://www.r-project.org

Docker image for kraken2 available at: https://github.com/DerrickWood/kraken2

Docker image for somalier available here: https://github.com/brentp/somalier

Docker image for BBTools available here: https://github.com/bbushnell/BBTools

Docker image for telseq available at: https://github.com/zd1/telseq

preseq availabe at: https://github.com/smithlabcode/preseq

VerifyBamID available at: https://griffan.github.io/VerifyBamID/

Docker image for multiqc available here: https://github.com/ewels/MultiQC

Docker image for fastp available here: https://github.com/OpenGene/fastp

R package available here: https://github.com/genome/sciclone

Calculate sequence coverage depth

Docker image for picard available at: https://github.com/broadinstitute/picard

Docker image for kallisto available at: https://github.com/pachterlab/kallisto

Docker image for fgbio available at: https://github.com/fulcrumgenomics/fgbio

Base image for bioinformatic analysis for which to build other images off of.

bam file utilities

Docker image for bedtools available at: https://github.com/arq5x/bedtools2

Docker image for optitype available at: https://github.com/FRED-2/OptiType

fragCounter software available at https://github.com/mskilab/fragCounter