kallisto

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

Overview

Dependencies

• kallisto 0.50.0

Usage

Cromwell

java -jar cromwell.jar run kallisto.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
fastqR1	File	Input fastqR1 file for analysis sample
fastqR2	File	Input fastqR2 file for analysis sample
outputFileNamePrefix	String	Output prefix, customizable.

Optional workflow parameters:

Parameter	Value	Default	Description

Optional task parameters:

Parameter	Value	Default	Description
runKallisto.modules	String	"kallisto/0.50.0 kallisto-transcriptome-index/0.50.0"	Names and versions of modules
runKallisto.timeout	Int	48	Timeout in hours, needed to override imposed limits
runKallisto.jobMemory	Int	12	Memory in Gb for this job

Outputs

Output	Type	Description
abundanceH5	File	{'description': 'a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length. This file can be read in by sleuth', 'vidarr_label': 'abundanceH5'}
abundanceTsv	File	{'description': 'a plaintext file of the abundance estimates. It does not contains bootstrap estimates.', 'vidarr_label': 'abundanceTsv'}
runinfoJson	File	{'description': 'a json file containing information about the run', 'vidarr_label': 'runinfoJson'}

Commands

This section lists command(s) run by WORKFLOW workflow

• Running WORKFLOW

=== Description here ===.

<<< $KALLISTO_ROOT/bin/kallisto quant
-i $KALLISTO_TRANSCRIPTOME_INDEX_ROOT/transcriptome_kallisto0.50.0_ensembl104.idx
--bootstrap-samples=120
-o outputDir
-t 5
~{fastqR1}
~{fastqR2}

     mv outputDir/abundance.h5 ~{sampleID}.abundance.h5 
     mv outputDir/abundance.tsv  ~{sampleID}.abundance.tsv
     mv outputDir/run_info.json ~{sampleID}.run_info.json
 >>>

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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