Data Wrangling – C.bairdi NanoPore Reads Extractions With Seqtk on Mephisto

In my pursuit to identify which contigs/scaffolds of our C.bairdi” genome assembly from 20200917 correspond to interesting taxa, based on taxonomic assignments produced by MEGAN6 on 20200928, I used MEGAN6 to extract taxa-specific reads from cbai_genome_v1.01 on 20201007 – the output is only available in FastA format. Since I want the original reads in FastQ format, I will use the FastA sequence IDs (from the FastA index file) and provide that to seqtk to extract the FastQ reads for each sample and corresponding taxa.

This was run on my personal computer (mephisto) and documented in a Jupyter Notebook:

Jupyter Notebook (GitHub):