Awesome

simple-contig-joiner

Stitch contigs together by means of Mummer's nucmer and fill gaps with given reference sequence.

Requirements:

• Python 2.7 or 3.4 (might work on other versions as well)
• Mummer3: http://mummer.sourceforge.net/
• Testing requires Biopython

Limitations (see TODO.md):

• Currently for small genomes only only (reads all sequences into memory)
• No support for multiple chromosomes