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Old 10-07-2016, 05:03 AM   #5
Location: East Coast

Join Date: Jul 2016
Posts: 39

Originally Posted by bastianwur View Post
Yeah, that can for sure happen during the assembly processes, we've seen this during some comparative genomics tests.
But as suggested, use Pilon for error correction afterwards. It needs the reads mapped to the assembly, and will then check if the majority of the reads agree with the assembly, and will correct it if it's not the case.
The tool is relatively easy to use, in case you're familiar with the command line and know what a BAM file and a fasta file is.
Thanks Bastian. Which de novo assemblers do you use? Many do not appear to save the reads; the output is a contig consensus sequence (Tadpole & Velvet, for instance). The only one that I've used the saves the aligned reads with the assembled contig is the assembler within Geneious. I'd be interested to hear what you use.

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