Question: Link for pre-indexed BWA indices for human reference
0
gravatar for biokoala
11 weeks ago by
biokoala3.6k
biokoala3.6k wrote:

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

index human bwa reference genome • 168 views
ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by biokoala3.6k
2
gravatar for arup
11 weeks ago by
arup850
India
arup850 wrote:

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

ADD COMMENTlink written 11 weeks ago by arup850

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.

ADD REPLYlink written 11 weeks ago by biokoala3.6k

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.

ADD REPLYlink written 11 weeks ago by arup850

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

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by biokoala3.6k
0
gravatar for dariober
11 weeks ago by
dariober9.9k
Glasgow - UK
dariober9.9k wrote:

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)

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by dariober9.9k
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