Hello everyone,
I am trying to figure out if there is a contamination in my Illumina reads which have bimodal GC content per sequence. I quality filtered to have enough reads with a decent length with optimal quality. Only problem is my bimodal GC content.
Is it normal to suspect a contamination? I am trying to plot the GC content in every contig of my Megahit assembly. I am trying to use python dictionary function to create bins out of it but I really lack the knowledge on how to use it. Can you help me out with this? Thanks everyone.
2 answers
You can map the reads to reference genome, keep unmapped reads and do blast against nr database to find out any contamination. In my case with plant de novo transciptome assembly, after making assembly and blasting against nr database, I found which contamination I have, so I removed the corresponding reads by bbmap and re-analyzed the clean reads.
Can't help with Python bins. We have viral reads and filter out any human contamination. This is done by mapping the reads to an indexed file with both human reference genome and a viral database. Any read that maps to human gets discarded. Any read that maps to viral gets kept.
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