Kalisto is a program for quantifying abundances of transcripts from RNA-Seq data. For more information, see the tool's GitHub repo. Toolchest only supports running kallisto quant with pre-built indexes at this time.

Function Call

tc.kallisto(
    inputs=[]
    output_path=None,
    tool_args="",
    database_name="kallisto_homo_sapiens",
    database_version="1",
    gtf=None, 
    chromosomes=None,
    is_async=False,
)

Function Arguments

Argument	Use in place of:	Description
`inputs`		Path or list of paths to input files for the Kallisto run. The files can be local or remote, see Using Files.
`output_path`	output file location	(optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be local or remote, see Using Files.
`tool_args`	all other arguments	(optional) Additional arguments to be passed to Kallisto. This should be a string of arguments like the command line.
`database_name`	`-i`, `--index`	(optional) Name of database to use for Kallisto alignment. Defaults to `"kallisto_homo_sapiens"`.
`database_version`	`-i`, `--index`	(optional) Version of database to use for Kallisto alignment. Defaults to `"1"`.
`gtf`	`-g`, `--gtf`	(optional) path to a GTF file for transcriptome information (required when using `--genomebam` tool arg). See the Kallisto manual for more info.
`chromosomes`	`-c`, `--chromosomes`	(optional) Path to a tab separated file with chromosome names and lengths (recommended when using `--genomebam` tool arg). See the Kallisto manual for more info.
`is_async`		Whether to run a job asynchronously. See Async Runs for more.

See the Databases section for more details.

Notes

Single-end inputs

Single-end read inputs require --single, --fragment-length (or -l), and --sd (or -s) to be provided via tool_args. See the Kallisto manual for more info.

Tool Versions

Toolchest currently supports version 0.48.0 of Kallisto.

Databases

Toolchest currently supports the following databases for Kallisto:

`database_name`	`database_version`	Description
`kallisto_homo_sapiens`	`1`	Homo sapiens Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_caenorhabditis_elegans`	`1`	Caenorhabditis elegans Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_danio_rerio`	`1`	Danio rerio Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_drosophila_melanogaster`	`1`	Drosophila melanogaster Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_gallus_gallus`	`1`	Gallus gallus Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_mus_musculus`	`1`	Mus Musculus Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_pan_troglodytes`	`1`	Pan Troglodytes Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_rattus_norvegicus`	`1`	Rattus norvegicus Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_saccharomyces_cerevisiae`	`1`	Saccharomyces cerevisiae Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
`kallisto_xenopus_tropicalis`	`1`	Xenopus tropicalis Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.

Other modes

Only quant mode is supported at this time.