Per base sequence content of Metagenomic samples
I am carrying out taxonomic classification of some metagenomic WGS samples (sequenced using Illumina NovaSeq and NexteraPE adaper libraries) using Kraken2 and I have a couple of questions related to the per base sequence content of some of these samples after quality control,
- One of the samples had this particular per base sequence content (image below). The bias observed in the content, can this be a result of duplicate reads? Note: While this particular sample had around 50% duplicate reads some samples that had similar per base sequence content but only had around 10 - 20% duplicate reads.
- Is it advisable to use such samples in taxonomic classification?
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Savindu •
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It is possible (assuming nothing else has gone wrong in the experiment) that your samples have low diversity. That combined with ample amplification will result in high duplicates.