Clean Module

The clean module provides functions for cleaning and preparing genome assemblies for annotation.

Key Functions

clean

This is the main function for cleaning and preparing genome assemblies. It takes a genome FASTA file as input and produces a cleaned FASTA file as output.

check_inputs

Checks that the input files exist and are valid.

clean_header

Cleans FASTA headers by removing unwanted characters and optionally slicing at a specified character.

filter_contigs

Filters contigs by minimum length.

sort_contigs

Sorts contigs by size or name.