Lib.rs

nons is a simple and hopefully not too slow program to fill Ns in contigs, by taking the consensus of reads aligned to these contigs.

To run it, take your sorted BAM file (perhaps created with BamM) and run nons:

nons contigs_with_Ns.fna reads_aligned_to_contigs_with_Ns.bam >filled_contigs.fna

filled_contigs.fna should now contain no Ns, unless there was no Ns aligned at those positions.

Install

After installing rust, install nons through cargo

cargo install nons

Help

Probably the easiest would be to raise an issue on GitHub or contact the author directly.

License

nons is written by Ben Woodcroft (@wwood) at the Australian Centre for Ecogenomics (UQ) and is licensed under GPL3 or later. A copy of the LICENSE is included in the repository.