How to get the species abundance in metagenomic data sequenced by PacBio/Nanopore?
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11 months ago
u9313025 • 0

Hello Experts,

I am working with some microbial metagenomic data. As the third-generation sequencer be come more famous. I wonder if there is any method to get the species abundance in metagenomic data sequenced by PacBio or Nanopore ? In short-read platform, I am using bwa to map the reads to the contigs and count the read depth as raw abundance. But how it will be in long read platform? Can I use the same strategy to get the abundance? (ex: minimap2) or there is a better way to do it.

Thank you.

metagenome metagenomic pacbio nanopore • 389 views
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