Seqer

Return .fasta containing records smaller than or larger than desired length.

This script is designed to be run on files in .fasta format

Dependencies:

• Python3
• Biopython

export PATH=$PATH:[PATH TO Seqer]

Usage

python short_seqer.py or long_seqer.py <desired length in bp (integer)> <assembly.fasta>

If no arguments are provided, the script will return help message.

Outputs

• .fasta file containing sequences shorter or longer than desired length

Citation

If this script is useful to you, please cite the following in your publication:

@software{Seqer,
  author = {Sim, Sheina B.},
  title = {Seqer},
  url = {https://github.com/sheinasim/seqer}
}

Sheina B. Sim
USDA-ARS
US Pacific Basin Agricultural Research Service
Hilo, Hawaii, 96720 USA
sheina.sim@usda.gov

This script is in the public domain in the United States per 17 U.S.C. § 105