Contigs have different mutations than raw reads
Hi,
I ran two assembly softwares and called mutations from the contigs. However, when I compared the contigs with raw reads, I found some instances where raw reads does not have mutations but the contigs have. I don't know how to explain this. Please see the attached.
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Ram
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Rashedul Islam
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Rashedul Islam
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Which assemblers did you run and how?
The first one is megahit ($megahit -1 fastq1 -2 fastq2 -o /path/) and second one is metaspades ($metaspades.py -1 fastq1 -2 fastq2 -o /path/). Reads were trimmed with Trimmomatic. Its an RNA virus genome.