Data Wrangling - FastA Splitting With faSplit

2019
Miscellaneous
Author

Sam White

Published

July 31, 2019

Steven posted an issue on GitHub regarding splitting a FastA file into multiple sequences. Specifically, he wanted a single, large FastA sequence (~89Mbp) split into smaller FastAs for BLASTing.

I downloaded the FastA he provided (https://d.pr/f/UlzHLR) and split the sequence into 2000bp chunks using the faSplit program (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/):

faSplit \
size \
20190731_faSplit_PGA-scaffold1_splits_2000bp/ \
2000

RESULTS

Output folder:

This produced 38,734 FastA files.