Filtering Contigs by Coverage

[MicroBio]

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!

[nickloman]

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.

[MicroBio]

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!

[AdrianP]

Mira does it automatically, and so do most kmer based assemblers, they put coverage in terms of kmer coverage.