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

Function Call

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

Function Arguments

ArgumentUse in place of:Description
inputsPath or list of paths to input files for the Kallisto run. The files can be local or remote, see Inputs and Outputs.
output_pathoutput 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 Inputs and Outputs.
tool_argsall 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_asyncWhether 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_namedatabase_versionDescription
kallisto_homo_sapiens1Homo sapiens Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_caenorhabditis_elegans1Caenorhabditis elegans Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_danio_rerio1Danio rerio Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_drosophila_melanogaster1Drosophila melanogaster Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_gallus_gallus1Gallus gallus Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_mus_musculus1Mus Musculus Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_pan_troglodytes1Pan Troglodytes Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_rattus_norvegicus1Rattus norvegicus Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_saccharomyces_cerevisiae1Saccharomyces cerevisiae Ensembl v96 index for Kallisto, pulled from https://github.com/pachterlab/kallisto-transcriptome-indices/releases/tag/ensembl-96.
kallisto_xenopus_tropicalis1Xenopus 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.


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