Take in an assembly in FASTA format, reads in FASTQ format, and optionally a reference and produce a better reference using Abacas/SSpace and GapFiller.
Scaffolding is performed using SSpace, and gap closing is performed using GapFiller. Both must be downloaded from http://www.baseclear.com [Optional] Contig Ordering is performed using Abacas, and requires nucmer and promer to be installed.