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Updated Oct 19, 2026

Utilities

Estimate transcript abundance with kallisto

kallisto-quant is an offline RNA-seq transcript quantification node.

Agent
Quantify single-end readsQuantify paired-end readsRetain native run counts

overview

What kallisto-quant does

Supply transcript FASTA and one sample of FASTQ reads to build a local index and estimate transcript abundance.

The adapter runs kallisto index and quant and returns native abundance.tsv, run_info.json and a log. Single-end reads require fragment-length and sd; paired-end data uses read1 and read2. The index is rebuilt for this job.

Use uncompressed FASTQ and at most 128 MiB per input file. Each native step has a 300-second limit. This contract exposes no bootstrap analysis and makes no network calls. Counts and TPM are estimates for the supplied reference and settings.

This packaged operation uses 0.52.0. Upstream license: BSD-2-Clause. The linked source identifies the actual program; this page documents the adapter's exposed contract.

source github.com/pachterlab/kallisto/tree/v0.52.0

use cases

Where kallisto-quant fits

Quantify single-end reads

Provide mean fragment length and standard deviation for single-end reads.

Quantify paired-end reads

Supply read1 and read2 for one paired-end sample.

Retain native run counts

Keep native abundance estimates beside processed and pseudoaligned read counts.

reference

kallisto-quant inputs and flags

6 inputs
NameTypeFlagDescription
sourceFOLDER--sourceFolder of transcript FASTA and uncompressed FASTQ reads.
transcriptsSTRING--transcriptsRelative transcript FASTA path (at most 128 MiB).
read1STRING--read1Relative single-end or first paired-end FASTQ path (at most 128 MiB).

Showing key inputs. kallisto-quant exposes 6 inputs in total.

Full flag reference (6 inputs)
NameTypeFlagDescription
sourceFOLDER--sourceFolder of transcript FASTA and uncompressed FASTQ reads.
transcriptsSTRING--transcriptsRelative transcript FASTA path (at most 128 MiB).
read1STRING--read1Relative single-end or first paired-end FASTQ path (at most 128 MiB).
read2STRING--read2Optional second paired-end FASTQ path.
fragment-lengthSTRING--fragment-lengthSingle-end mean fragment length, 1-10000 (required for single-end).
sdSTRING--sdSingle-end fragment length standard deviation, greater than 0 and at most 10000.

example

Run kallisto-quant

kallisto-quant · command
python3 /app/run.py --source ./source --transcripts transcripts.fasta --read1 reads.fastq --fragment-length 150 --sd 20 ./output

guidance

Choosing kallisto-quant

Use kallisto for one sample against a supplied transcript reference. Sequence alignment, differential expression and biological interpretation require separate analysis.

faq

kallisto-quant questions

source: Folder of transcript FASTA and uncompressed FASTQ reads. transcripts: Relative transcript FASTA path (at most 128 MiB). read1: Relative single-end or first paired-end FASTQ path (at most 128 MiB). read2: Optional second paired-end FASTQ path. fragment-length: Single-end mean fragment length, 1-10000 (required for single-end). sd: Single-end fragment length standard deviation, greater than 0 and at most 10000.

Abundance TSV and run info. The adapter runs kallisto index and quant and returns native abundance.tsv, run_info.json and a log. Single-end reads require fragment-length and sd; paired-end data uses read1 and read2. The index is rebuilt for this job.

Use uncompressed FASTQ and at most 128 MiB per input file. Each native step has a 300-second limit. This contract exposes no bootstrap analysis and makes no network calls. Counts and TPM are estimates for the supplied reference and settings.

Use kallisto for one sample against a supplied transcript reference. Sequence alignment, differential expression and biological interpretation require separate analysis.

The public image repository includes download instructions for this version and a separate source/notices bundle. Its overview provides an immutable ORAS command, the expected bundle checksum and pinned upstream source directions. The bundle contains the original build recipe, runtime sources and retained component license notices. Image, source and license notice downloads.

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Run kallisto-quant yourself

The saved synthetic check verified 60 processed and 60 pseudoaligned reads, with estimated counts near 40 and 20 for two synthetic transcripts. The full abundance TSV is not retained as a page sample. The command shows the container entrypoint with example paths.

Open kallisto-quant in the libraryBuild a workflow with it

Facts on this page come from the live Trickest tool library.