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Old 10-06-2016, 07:19 AM   #4
Location: Germany/Netherlands

Join Date: Feb 2014
Posts: 98

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.
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