Consensus sequence from SAM or BAM file?
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2.1 years ago
lokraj2003 ▴ 90

I am trying to perform reference-based assembly. Most of the tutorials teach how to create a bam file and view alignemnts in IGV or Tablet. But, I want a assembled genome sequence in fasta format. How can I do that ? Is there any tool or linux syntax available for this purpose ?

assembly • 957 views
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But, I want a assembled genome sequence in fasta format.

Assembling a genome is not what you get by aligning to a reference. For that, you need an assembler.

Creating a consensus from an alignment will also give you a fasta consensus, but it is not the same as a real de novo assembly.

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Hello lokraj2003!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/7441/consensus-sequence-from-sam-or-bam-file

This is typically not recommended as it runs the risk of annoying people in both communities.

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