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Question: Bowtie2 mapping of (several, long) contigs in fasta to a reference sequence - contig sequences only mapped as 60 bp
0
gravatar for kalfsnes
2.7 years ago by
kalfsnes • 10
kalfsnes • 10 wrote:

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.
sequence alignment bowtie2 de novo • 1.7k views
ADD COMMENT • link •
written 2.7 years ago by kalfsnes • 10
3
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan ♦ 94k
Freiburg, Germany
Devon Ryan ♦ 94k wrote:
  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.
ADD COMMENT • link written 2.7 years ago by Devon Ryan ♦ 94k
  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! :-)
ADD REPLY • link written 2.7 years ago by kalfsnes • 10
1

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.

ADD REPLY • link written 2.7 years ago by Devon Ryan ♦ 94k
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