BWA align contigs with Clustal-like output
1
0
Entering edit mode
5.1 years ago
biotech ▴ 540

Is it possible to have BWA align contigs to reference and have output visualised via IGV/Tablet with Gaps and SNPs highlighted?

I'm trying this strategy because I need to visualise alignment of 10-20 regions of the reference genome but don't have this regions in separated fasta files for other strains we want to identify SNPs/indels for some reference coordinates. All bacterial data is already assembled.

BWA SNPs Clustal • 1.5k views
ADD COMMENT
0
Entering edit mode

You may be able to use Mauve for this without doing alignments with bwa.

ADD REPLY
0
Entering edit mode
5.1 years ago

Is it possible to have BWA align to contigs to the reference...

Yes

...and have output visualised via IGV/Tablet...

BAM format

...with Gaps and SNPs highlighted?

In IGV differences are colored by default. Indels are also marked. I assume Tablet does something similar, I've never used it.

ADD COMMENT

Login before adding your answer.

Traffic: 1139 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6