Masking Uncovered Segments Of Assembled Contig

Question

[2184687-1231-83-]

Hi,

I've got contigs assembled from a read set, and I want a simple tool that, for a subset of the reads, will map again to the contig and mask with NNNs those parts of the contig that are not covered by the read subset.

What would be a good tool for that?

I've been told I should script around pileup, but I refuse to think there isn't an easier way of doing it already.

Cheers

[Eric Normandeau]

Hi @Avilella. What kind of format are the data in? .fasta? .ace? Are there low quality ends on your assembled sequences (such as would be described in an .ace file) that should not be included in your mapped region of the contigs? Would you accept a Python solution using Biopython or do you absolutely want an already made program? Cheers!

Answer 1

[Pierre Lindenbaum]

maskFastaFromBed from the bedtools? See here

Answer 2

[2184687-1231-83-]

Answering my own question, I actually ended up using maq easyrun and using the consensus sequence.

perl ~/src/maq/maq-0.7.1/scripts/maq.pl easyrun -d outdir 327.columbus/contigs.fa 286557.reads