Skip to content

Python scripts designed to perform tasks associated with the pangenome construction method of iterative mapping and assembly

License

Notifications You must be signed in to change notification settings

AppliedBioinformatics/pangenome

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

9 Commits
 
 
 
 
 
 
 
 

Repository files navigation

Supplementary script for book chapter: Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach

Remove_reads_with_Ns.py

This script is used to remove paired raw reads with unknown bases (Ns) as these reads will affect the performance of mapping and end up in the pool of unmapped reads – the assumption being that the sequencing run’s quality was good enough to have only few reads with Ns.

Usage:python Remove_reads_with_Ns.py [--cutoff CUTOFF] R1 R2

splitUp.py

This script is used to split the unmapped fastq files into R1, R2 and singlets for assembly by MaSuRCA.

Usage: python splitUp.py R1.fastq R2.fastq

This will create three files, one with the R1, one with the R2, and one with the singlets. Use all three in Masurca

About

Python scripts designed to perform tasks associated with the pangenome construction method of iterative mapping and assembly

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages