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Reference transcriptome indices build from kallisto for popular organisms
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kallisto indices indices constructed from Ensembl reference transcriptomes. Downloads available from the releases page.

Building indices with kallisto

To build the indices, download the full transcriptomes from Ensembl (files ending in cdna.all.fa.gz) and build the indices with kallisto.

For example, to build the human transcriptome index, first download the transcriptome, which is available under cDNA on the Ensembl website, at

curl -O

Then run kallisto index. kallisto will work on .fa and .fz.gz files so there is no need to unzip the downloaded file:

kallisto index -i 	Homo_sapiens.GRCh38.cdna.all.release-94_k31.idx	Homo_sapiens.GRCh38.cdna.all.fa.gz

Indices avaialble here were built with the default --kmer-size=31. A different k-mer size can be chosen using the -k or --kmer-size option (odd k only). A full description of the command can be obtained by typing kallisto index:

kallisto 0.45.0
Builds a kallisto index

Usage: kallisto index [arguments] FASTA-files

Required argument:
-i, --index=STRING          Filename for the kallisto index to be constructed 

Optional argument:
-k, --kmer-size=INT         k-mer (odd) length (default: 31, max value: 31)
    --make-unique           Replace repeated target names with unique names
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