Does the Bioinformatics Toolbox R2023b ship with BWA index files for the human genome?

I want to use the "bwamem" function for human genome. Does MATLAB R2023b ship with index files for human genome? (e.g. for Build37)

Answer 1

[MathWorks Support Team]

The Bioinformatics Toolbox R2023b does not ship with BWA index files for the human genome. There are a number of publicly available databases for downloading Build37, from which you can generate the bwa indices:

https://www.ncbi.nlm.nih.gov/genome/guide/human/

https://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/

https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/

An example of downloading and indexing Build37 with "bwaindex" is given below: 

GRCH37File = websave("GRCh37_latest_genomic.fna.gz", "https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.fna.gz");
GRCH37BwaIndexPrefix = "GRCH37BwaIndex"
bwaindex(GRCH37File, Prefix=GRCH37BwaIndexPrefix)