The script concoct_coverage_table.py will use samtools bedcov and a bedfile to get coverage for regions specified in the bedfile. This makes it possible to use subcontigs specified in the bedfile instead of redoing the mapping onto subcontigs. Instructions are given in the README.
The cut_up_fasta.py script is modified to be able to construct this bedfile.
The script
concoct_coverage_table.pywill use samtools bedcov and a bedfile to get coverage for regions specified in the bedfile. This makes it possible to use subcontigs specified in the bedfile instead of redoing the mapping onto subcontigs. Instructions are given in the README.The
cut_up_fasta.pyscript is modified to be able to construct this bedfile.