Question: index reference BWA
gravatar for manubiomed20
5 weeks ago by
manubiomed200 wrote:

Can someone help me with the index of reference using BWA?

First, I am not understanding anything of the command quoted by the tutorial that is indicated for index: bwa index [-p prefix] [-a algoType] <in.db.fasta>

I do not understand what exit database prefix means or what it means -a. I've read the manual and I'm not clear.

Another thing I do not understand is how I will select the reference sequence to index. Help-me

assembly • 165 views
ADD COMMENTlink modified 5 weeks ago by h.mon25k • written 5 weeks ago by manubiomed200
gravatar for Kevin Blighe
5 weeks ago by
Kevin Blighe42k
Kevin Blighe42k wrote:

The options for bwa index are :

bwa-0.7.17/bwa index

Usage:   bwa index [options] <in.fasta>

Options: -a STR    BWT construction algorithm: bwtsw, is or rb2 [auto]
         -p STR    prefix of the index [same as fasta name]
         -b INT    block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]
         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.*

The standard option for human and mouse would be -a bwtsw, which creates indices based on the Burrows-Wheeler Transform (BWT).

Thus, to index your FASTA genome, you just need to do:

bwa-0.7.17/bwa index -a bwtsw mm10/mm10.fasta

[bwa_index] Pack FASTA... 52.54 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5461743548, availableWord=396308404
[BWTIncConstructFromPacked] 10 iterations done. 99999996 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999996 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999996 characters processed.
... ...
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Kevin Blighe42k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1474 users visited in the last hour