v1

v1 of indices (supports kallisto versions >= 0.50.1)

The indices are enclosed in the .tar.xz files.

The actual FASTA sequences are uploaded as well: .mature.fa.gz for the sequences indexed for the "standard" index and equivalent to the "mature" transcripts in the "nac" index, and .nascent.fa.gz for the "nascent" transcripts in the "nac" index.

Ensembl Transcriptomes v96

These index files were produced using kallisto version 0.45.1 on Ensembl v96 transcriptomes. The transcripts_to_genes.txt files were made with t2g.py (see file below).

Each "tarball" https://en.wikipedia.org/wiki/Tar_(computing) contains

1. kallisto index transcriptome.idx
2. Species GTF file from Ensembl species.gtf
3. Species cDNA FASTA file from Ensembl species.fa
4. Transcripts to Genes Map (w/ version numbers) transcripts_to_genes.txt for use with kallisto | bustools

Caenorhabditis elegans
Danio rerio
Drosophila melanogaster
Gallus gallus
Homo sapiens
Mus musculus
Pan troglodytes
Rattus norvegicus
Saccharomyces cerevisiae
Xenopus tropicalis

Ensembl Transcriptomes v94

These index files were produced using kallisto version 0.45.0 for the following transcriptomes:

Caenorhabditis elegans
Danio rerio
Drosophila melanogaster
Gallus gallus
Homo sapiens
Mus musculus
Pan troglodytes
Rattus norvegicus
Saccharomyces cerevisiae
Xenopus tropicalis

The transcriptomes were downloaded as cDNA fasta files from the Ensembl data repository at https://uswest.ensembl.org/info/data/ftp/index.html