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Masking Uncovered Segments Of Assembled Contig

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

assembly reference
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written by 2184687-1231-83- 2184687-1231-83-

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!

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written by Eric Normandeau Eric Normandeau

2 answers

maskFastaFromBed from the bedtools? See here

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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
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updated by Ram Ram • written by 2184687-1231-83- 2184687-1231-83-

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