Burrows Wheeler Aligner - tool
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5.3 years ago
sruthi ▴ 40

Hi, I'm new to BWA tool. I indexed my reference.fa using command:

bwa index -a bwtsw reference.fa reference_prefix

and got 3 output files: .amb .ann .pac

I read that the above command must produce 8 output files such as .amb .ann .bwt .pac .rbwt .rpac .rsa .sa.

As only 3 output files have been generated, has the command run successfully? If not what should I do?

TIA

alignment sequencing • 1.4k views
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bwa index output some messages to the screen, what did they say?

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Hey, So the messages displayed are: 1. bwa_index Pack FASTA 2. Construct BWT for the packed sequence 3. BWT_gen 4. Update BWT 5. Pack forward only FASTA 6. Construct SA from BWT and Occ...

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What is the reason that you chose bwtsw ?

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Hey, I chose bwtsw as the genome I'm analysing is of larger size, say 3.3 GB. Hence.

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5.3 years ago
Joe 21k

That command produces 5 files for me: .amb, .ann, .bwt, .pac and .sa.

bwa Version: 0.7.17-r1188

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Hey healey, I ran the command for the second time and got all these 5 files as the output. Thanks.

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