Skip to content

Latest commit

 

History

History
44 lines (29 loc) · 1.29 KB

README.md

File metadata and controls

44 lines (29 loc) · 1.29 KB
Raw

YACaSSF: Yet Another Contig and Scaffold Stat Finder

Report number of assembly pieces (contigs or scaffolds) and length of piece to make up a genome percentage of your choosing.

This script is designed to be run on a genome assembly in .fasta format

Dependencies:

  • Python3
  • Biopython
  • Python pandas package

export PATH=$PATH:[PATH TO YACaSSF]

Usage

python nlStats.py <genome percentage as an integer (50 for N50, 95 for N95)> <assembly.fasta> [Optional: --noheader (stdout has no header, good for running in for loop with multiple assemblies) default: header]

(pipe to column -t for more uniform looking tab separated output)

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

Outputs

  • Number of pieces and length of piece required for a percentage of your assembly size of your choosing as stdout

Citation

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

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

Sheina B. Sim
USDA-ARS
US Pacific Basin Agricultural Research Service
Hilo, Hawaii, 96720 USA
[email protected]

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