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Old 09-23-2013, 06:42 AM   #1
MicroBio
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Question Filtering Contigs by Coverage

Hi all,

I have a dataset where I assembled sequences into contigs and would now like to filter the contigs by coverage. My goal is to remove the contigs with low sequence coverage so that I can work only with those contigs with high coverage.

I am wondering if anybody knows if this is implemented in an existing sequence analysis program or something? I know I could write some code myself to do this, but I figured it was worth asking if anybody knows of this already existing? I haven't been able to find something that does this.

Thanks for your help!
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Old 09-23-2013, 07:36 AM   #2
nickloman
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Which assembler did you use? Some will output this information in the FASTA header, or in a separate statistics file, in which case it is easy to write a script to extract the ones you want. Otherwise you will need to align the reads back to the contigs to get this info.
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Old 09-23-2013, 08:10 AM   #3
MicroBio
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Thanks nickloman,

I used IDBA-UD. I'll look into whether or not it will give me that output like you mentioned. Otherwise I will go ahead and re-align the reads and deal with it from there. I was just curious if there were already programs to do this, and it looks like the answer is that some assemblers do this automatically. Thanks for the answer!
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Old 09-24-2013, 08:29 PM   #4
AdrianP
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Mira does it automatically, and so do most kmer based assemblers, they put coverage in terms of kmer coverage.
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