Data Wrangling - FastA Splitting With faSplit

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 ( and split the sequence into 2000bp chunks using the faSplit program (

faSplit \
size \
20190731_faSplit_PGA-scaffold1_splits_2000bp/ \


Output folder:

This produced 38,734 FastA files.