This script removes contaminants flagged during GenBank's submission process.
usage: genbank-submission-cleaner.py [-h] genbank_report input_genome clean_genome_output
Remove contaminants flagged during GenBank's submission process.
positional arguments:
genbank_report GenBank's contamination record file.
input_genome Genome to be cleaned.
clean_genome_output Directory where the cleaned genome will be written to.
optional arguments:
-h, --help Show this help message and exit
It takes as input the contamined genome (input_genome) and the GenBank's contamination report (genbank_report), which should end with something like this:
(…)
Trim:
Sequence name, length, span(s), apparent source
contig_1 3795 3754..3795 adaptor:NGB00360.1
contig_2 2219 2197..2219 adaptor:NGB01096.1
contig_3 2039 2010..2039 adaptor:NGB01088.1
contig_4 2228 2210..2228 adaptor:NGB01088.1
contig_5 2024 1..20 adaptor:NGB01088.1
contig_6 3074 3049..3074 adaptor:NGB01096.1