Quantify abundances of transcripts from bulk and single-cell RNA-Seq data.

Quick Start

$ pbrun kallisto \
    --ref Homo_sapiens_assembly38.fasta \
    --in-fq input1.fastq \
    --index /path/to/kallisto/index \
    --index-out output_index_file \
    --output-dir output_directory

kallisto Reference

Quantify abundances of transcripts from bulk and single-cell RNA-Seq data.

Input/Output file options

--index INDEX

Path to the kallisto index file generated from a reference file. If you have not indexed a reference file with kallisto, first create one with the "--ref" and "--index-out" arguments. (default: None)

Option is required.

--ref REF

Path to the reference file to create a kallisto index. (default: None)

--index-out INDEX_OUT

Path to the output kallisto index. (default: None)

--in-fq [IN_FQ [IN_FQ ...]]

Path to the pair ended FASTQ files. (default: None)

--output-dir OUTPUT_DIR

Path to the directory to write output. (default: None)

Options specific to this tool


Perform sequence based bias correction. (default: None)


Search for fusions for Pizzly. (default: None)


Number of bootstrap samples. (default: 0)

--num-threads NUM_THREADS

Number of threads to use. (default: 4)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)


Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.


Do not override seccomp options for docker (default: None).


View compatible software versions.