premade BWA hg38 index

Question

[marongiu.luigi]

Hello, is it possible to download premade GRCh38/hg38 BWA indices? like there are premade indices for STAR [http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STARgenomes/].Thank you

Answer 1

[h.mon]

Illumina iGenomes includes Bowtie / Bowtie2 / BWA indices, but be careful and check the genome of interest: for example, for a while, Bos taurus was missing chromosome 29. Also, the annotation tends to get outdated.

[marongiu.luigi]

I got the GRCh38 [ftp://igenome:[e-mail]/Homo_sapiens/NCBI/GRCh38/Homo_sapiens_NCBI_GRCh38.tar.gz] which contains genome.fa and other 5 files (amb, ann, bwt, pac and sa) but all at 1 KB. Shall I use the ones stored in the directory version0.6.0, i presume? These are much bigger.

[GenoMax]

The small files you refer to are soft links to the actual files that are contained in the version 0.6.0 directory.

Answer 2

[dariober]

At the end of the day making the index yourself is a better option I think. You are sure what genome you are indexing and what version of bwa you are using. When it comes to documenting or publishing your work it's one dependency less you have to care about since you don't have to state where you got the indexes from (and what if the URL links are removed?).

[marongiu.luigi]

I know, but at the moment i have a PC with low capability. I need the indices to test the script I am writing... and if they work I don't have to compute them anymore, I can simply download them when needed.

[GenoMax]

Get the bundle from iGenomes that @h.mon linked above then.