Question: Link for pre-indexed BWA indices for human reference
1
gravatar for lakhujanivijay
8 months ago by
lakhujanivijay4.3k
India
lakhujanivijay4.3k 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 • 366 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by lakhujanivijay4.3k
2
gravatar for arup
8 months ago by
arup1.5k
India
arup1.5k 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 8 months ago by arup1.5k

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 8 months ago by lakhujanivijay4.3k

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 8 months ago by arup1.5k

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

ADD REPLYlink modified 8 months ago • written 8 months ago by lakhujanivijay4.3k
0
gravatar for dariober
8 months ago by
dariober10k
WCIP | Glasgow | UK
dariober10k 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 8 months ago • written 8 months ago by dariober10k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 741 users visited in the last hour