This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Bowtie2 mapping of (several, long) contigs in fasta to a reference sequence - contig sequences only mapped as 60 bp

I've got contigs from de novo (Spades) assembly (approx 175 contigs of length 200 bp to 11 kb), and want to map these to a reference sequence and make a new consensus. I have tried using Bowtie2 and I do get an output. However, all the aligned contigs have been truncated down to 60 bp.

I've tried changing the Bowtie2 index to "large index", Bowtie2 is run using the -f and -U options.

Any help appreciated.

bowtie2 de novo sequence alignment
• 5,324 views • link
written by kalfsnes • kalfsnes

1 answer

  1. Does your fasta file have 60 base wide lines?
  2. You don't need a large index.
  3. I would strongly recommend that you use bwa (or minimap2) instead. It's unclear how good bowtie2 will be with long contigs.
• 0 views • link
written by Devon Ryan Devon Ryan
  1. Yes, but shouldn't Bowtie2 handle these line breaks? Anyway, I removed them, but that left me with a new problem - memory. I'll try run it on computer with more memory, see if that solves it.
  2. Okay.
  3. Worked like a charm with bwa - thanks! :-)
• 0 views • link
written by kalfsnes • kalfsnes

Nah, it expects sequences on a single line for fastq files, so fasta will be the same. I expect most aligners that accept fasta input are like that.

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this