See Releases page for a collection of popular reference genomes that have been bgzip'ed and indexed using samtools.
- 'hg19' hg19.fa.gz - [Source + README](https://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/). Build from UCSC.
- 'grch37' Homo_sapiens.GRCh37.dna.toplevel.fa.gz- [Source](https://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/). [README](https://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/README). Genome assembly: GRCh37.p13 (GCA_000001405.14)
- 'hg38' hg38.fa.gz - [Source + README](https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/). Build from UCSC.
- 'grch38' Homo_sapiens.GRCh38.dna.toplevel.fa.gz - [Source](https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/). [README](https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/README). Genome assembly: GRCh38.p14 (GCA_000001405.29)
- 't2t' hs1.fa.gz - [Source](https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/). [README](https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/GCA_009914755.4_assembly_report.txt). T2T-CHM13v2.0 with chrY from NA24385
- Mouse (Mus musculus)
'mm39' mm39.fa.gz - [Source + README](https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/). GRCm39/mm39 mouse genome (GCA_000001635.9)
- Fruit fly (Drosophila melanogaster)
'dm6' dm6.fa.gz - [Source + README](https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/). BDGP Release 6 + ISO1 MT/dm6
- Worm (Caenorhabditis elegans)
'ce11' ce11.fa.gz - [Source + README](https://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips/). WBcel235/ce11
- Chimpanzee (Pan troglodytes)
'pantro6' panTro6.fa.gz - [Source + README](https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/). Clint_PTRv2/panTro6
- Zebrafish (Danio rerio)
'danrer11' danRer11.fa.gz - [Source + README](https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips/). GRCz11/danRer11
- Yeast (Saccharomyces cerevisiae)
'saccer3' sacCer3.fa.gz - [Source + README](https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/)