dockstore-tool-bwa-mem

Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq] Algorithm options: -w INT band w...

dockstore-tool-bwa-samse

Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>

dockstore-tool-kallisto

Usage: Available at https://pachterlab.github.io/kallisto/manual.html

dockstore-tool-liftover

Move annotations from one assembly to another usage: liftOver oldFile map.chain newFile unMapped...

dockstore-tool-linux-sort

Usage: sort [OPTION]... [FILE]... or: sort [OPTION]... --files0-from=F Write sorted concatenation...

dockstore-tool-rnaseqc

Computes a series of quality control metrics for RNA-seq data. Usage: -bwa <arg> Path to BWA, whic...

dockstore-tool-samtools-index

Prints alignments in the specified input alignment file. Usage: samtools index [-bc] [-m INT] <in.b...

dockstore-tool-samtools-rmdup

Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only re...

dockstore-tool-samtools-sort

Sort alignments by leftmost coordinates, or by read name when -n is used. An appropriate @HD-SO sort...

dockstore-tool-samtools-view

Prints alignments in the specified input alignment file. With no options or regions specified, prin...

dockstore-tool-snpeff

Annotates and predicts the effects of variants on genes (such as amino acid changes).