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kallisto

A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.

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kallisto forum

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kallisto versioning

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kallisto classification

kallisto specifications

Software type:
Package/Module
Restrictions to use:
Academic or non-commercial use
Operating system:
Mac OS, Windows
Version:
0.42.1
Maintained:
Yes
Interface:
Command line interface
Input format:
FASTQ
Computer skills:
Advanced
Stability:
Stable
Conda:
https://bioconda.github.io/recipes/kallisto/README.html

kallisto support

Documentation

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