kallisto-transcriptome-indices

kallisto indices indices constructed from Ensembl reference transcriptomes version 108. Downloads available from the releases page. These indices apply to kallisto version >=0.50.1 (which is part of kb-python >=0.28.0).

List of species

Indices for five species are available: human (Homo sapiens), mouse (Mus musculus), dog (Canis lupus familiaris), monkey (Macaca mulatta), and zebrafish (Danio_rerio).

The genome FASTA files and GTF files used to generate the indices are listed below.

1. human

   Genome: https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz

   GTF: https://ftp.ensembl.org/pub/release-108/gtf/homo_sapiens/Homo_sapiens.GRCh38.108.gtf.gz

2. mouse

   Genome: https://ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz

   GTF: https://ftp.ensembl.org/pub/release-108/gtf/mus_musculus/Mus_musculus.GRCm39.108.gtf.gz

3. dog

   Genome: https://ftp.ensembl.org/pub/release-108/fasta/canis_lupus_familiaris/dna/Canis_lupus_familiaris.ROS_Cfam_1.0.dna.toplevel.fa.gz

   GTF: https://ftp.ensembl.org/pub/release-108/gtf/canis_lupus_familiaris/Canis_lupus_familiaris.ROS_Cfam_1.0.108.gtf.gz

4. monkey

   Genome: http://ftp.ensembl.org/pub/release-108/fasta/macaca_mulatta/dna/Macaca_mulatta.Mmul_10.dna.toplevel.fa.gz

   GTF: https://ftp.ensembl.org/pub/release-108/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.108.gtf.gz

5. zebrafish

   Genome: http://ftp.ensembl.org/pub/release-108/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz

   GTF: http://ftp.ensembl.org/pub/release-108/gtf/danio_rerio/Danio_rerio.GRCz11.108.gtf.gz

Types of indices

Two indices are supported:

1. The standard index (which does not contain introns and is therefore only suitable for quantifying bulk and single-cell RNA-seq)
2. The nac index (which contains both nascent transcripts and cDNAs and therefore can be used for applications where quantifying intron-spanning reads is important, such as single-nucleus RNA-seq or biophysical models that jointly consider spliced and unspliced transcripts).

Note: The term cDNA used throughout follows that of Ensembl. That is, the cDNA represents the sequences of the mature transcripts wherein introns are not included as they have been spliced out.

Contents of indices

Both the standard and nac index are packaged with the following two files:

• index.idx: The kallisto index that reads will be pseudoaligned against
• t2g.txt: A file containing the transcript-to-gene mapping

The nac index will be packaged with two additional files:

• cdna.txt: The IDs of the cDNA transcripts
• nascent.txt: The IDs of the nascent transcripts

Downloading the indices

While you could download the indices, you could use the kb ref command within kb-python to download the index. For example, to download the zebrafish indices, you would do:

# Standard index:
kb ref -d zebrafish -i index.idx -g t2g.txt
# nac index:
kb ref --workflow=nac -d zebrafish -i index.idx -g t2g.txt -c1 cdna.txt -c2 nascent.txt

How indices were generated

All indices were generated using kb-python 0.28.0 (with the kallisto 0.50.1 binary) with the respective species's genome FASTA (genome.fa.gz) and genome GTF annotation (genome.gtf.gz) as follows:

standard index

kb ref --workflow=standard -i index.idx -g t2g.txt -f1 cdna.fa \
  --include-attribute gene_biotype:protein_coding \
  --include-attribute gene_biotype:lncRNA \
  --include-attribute gene_biotype:lincRNA \
  --include-attribute gene_biotype:antisense \
  --include-attribute gene_biotype:IG_LV_gene \
  --include-attribute gene_biotype:IG_V_gene \
  --include-attribute gene_biotype:IG_V_pseudogene \
  --include-attribute gene_biotype:IG_D_gene \
  --include-attribute gene_biotype:IG_J_gene \
  --include-attribute gene_biotype:IG_J_pseudogene \
  --include-attribute gene_biotype:IG_C_gene \
  --include-attribute gene_biotype:IG_C_pseudogene \
  --include-attribute gene_biotype:TR_V_gene \
  --include-attribute gene_biotype:TR_V_pseudogene \
  --include-attribute gene_biotype:TR_D_gene \
  --include-attribute gene_biotype:TR_J_gene \
  --include-attribute gene_biotype:TR_J_pseudogene \
  --include-attribute gene_biotype:TR_C_gene \
  genome.fa.gz genome.gtf.gz

nac index

kb ref --workflow=nac -i index.idx -g t2g.txt \
  -f1 cdna.fa -f2 nascent.fa -c1 cdna.txt -c2 nascent.txt \
  --include-attribute gene_biotype:protein_coding \
  --include-attribute gene_biotype:lncRNA \
  --include-attribute gene_biotype:lincRNA \
  --include-attribute gene_biotype:antisense \
  --include-attribute gene_biotype:IG_LV_gene \
  --include-attribute gene_biotype:IG_V_gene \
  --include-attribute gene_biotype:IG_V_pseudogene \
  --include-attribute gene_biotype:IG_D_gene \
  --include-attribute gene_biotype:IG_J_gene \
  --include-attribute gene_biotype:IG_J_pseudogene \
  --include-attribute gene_biotype:IG_C_gene \
  --include-attribute gene_biotype:IG_C_pseudogene \
  --include-attribute gene_biotype:TR_V_gene \
  --include-attribute gene_biotype:TR_V_pseudogene \
  --include-attribute gene_biotype:TR_D_gene \
  --include-attribute gene_biotype:TR_J_gene \
  --include-attribute gene_biotype:TR_J_pseudogene \
  --include-attribute gene_biotype:TR_C_gene \
  genome.fa.gz genome.gtf.gz

Questions and Issues

Please use the issues section of the kallisto repo or the kb-python repo. Do not use the issues section of this repo.