kallisto is a program for quantifying abundances of transcripts from bulk and single-cell 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. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools. kallisto is described in detail in:
Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525–527 (2016), doi:10.1038/nbt.3519
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kallisto can process either single-end or paired-end reads. The default running mode is paired-end and requires an even number of FASTQ files represented as pairs, e.g.
For single-end mode you supply the
--singleflag, as well as the-land-soptions, and list any number of FASTQ files, e.gFASTQ files can be either plaintext or gzipped.
kallisto quantproduces three output files by default:--plaintextmode to output plaintext abundance estimates. Alternatively,kallisto h5dumpcan be used to output an HDF5 file to plaintext. The first line contains a header for each column, including estimated counts, TPM, effective length.