Description

Computes equivalence classes for reads and quantifies abundances

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

*.{fastq,fastq.gz}

index (file)

Kallisto genome index.

*.idx

gtf (file)

Optional gtf file for translation of transcripts into genomic coordinates.

*.gtf

chromosomes (file)

Optional tab separated file with chromosome names and lengths.

*.tsv

fragment_length (integer)

For single-end mode only, the estimated average fragment length.

fragment_length_sd (integer)

For single-end mode only, the estimated standard deviation of the fragment length.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

log (file)

File containing log information from running kallisto quant

*.log.txt

abundance (file)

Plaintext file of the abundance estimates

abundance.tsv

abundance_hdf5 (file)

A HDF5 binary file containing run info, abundance estimates, bootstrap
estimates, and transcript length information

abundance.h5

run_info (file)

A json file containing information about the run

run_info.json
included in
riboseq rnaseq
maintainer
Github user anoronh4
get in touch
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Tools

kallisto
BSD_2_clause

Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.

pachterlab.github.io/kallisto pachterlab.github.io/kallisto/manual https://github.com/pachterlab/kallisto 10.1038/nbt.3519