Data Wrangling - FastA Subsetting of Pgenerosa_v070.fa Using samtools faidx

Steven asked to subset the Pgenerosa_v070.fa (2.1GB) in this GitHub Issue #705. In that issue, it was determined that a significant portion of the sequencing data that was assembled by Phase Genomics clustered in “scaffolds” 1 - 18. As such, Steven asked to subset just those 18 scaffolds.

This was done by using the samtools faidx program.

Process is documented in the following Jupyter Notebook (GitHub):

• 20190625_swoose_pgen_v070_scaffolds.ipynb

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RESULTS

Output folder:

• 20190625_pgen_v070_scaffold_subsetting/

FastA (914MB):

• 20190625_pgen_v070_scaffold_subsetting/Pgenerosa_v070.18.fa

FastA Index: - 20190625_pgen_v070_scaffold_subsetting/Pgenerosa_v070.18.fa.fai