Link for pre-indexed BWA indices for human reference

Question

[lakhujanivijay]

I am looking for pre-indexed BWA indices for human reference. Found a similar post with only a little help (some links are broken)

Bwa Index On All Human Grch37 Sequences

Answer 1

[Arup Ghosh]

Illumina has a collection of "Ready-To-Use" reference sequences for commonly studied organisms which include the fasta reference sequence, Bowtie2 index, and BWA index files.

FIles: http://sapac.support.illumina.com/sequencing/sequencing_software/igenome.html?langsel=/in/

Documentation: ftp://ussd-ftp.illumina.com/README.txt

[lakhujanivijay]

Hi arup

Thanks for sharing the link. But, are you sure that contains BWA indices? What I could see are only fasta and annotation files? Also, that ftp (ftp://ussd-ftp.illumina.com/README.txt) asks for username and password.

[Arup Ghosh]

I've uploaded the contents of README.txt in github.

Sequence/BWAIndex/ contains an index of the whole genome for use with the BWA aligner. Since the BWA index scheme changed at version 0.6.0, both versions 0.5.x and 0.6.0 (and higher) are included.

[lakhujanivijay]

+1 for that arup. It worked!! Thanks a lot

Answer 2

[dariober]

Here?

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

In most cases, the recommended reference is the _no_alt_plus_ (based on this post by Heng Lee)