PT - JOURNAL ARTICLE AU - Jennifer M Shelton AU - Michelle C Coleman AU - Nic Herndon AU - Nanyan Lu AU - Ernest T Lam AU - Thomas Anantharaman AU - Palak Sheth AU - Susan J Brown TI - Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool AID - 10.1101/020966 DP - 2015 Jan 01 TA - bioRxiv PG - 020966 4099 - http://biorxiv.org/content/early/2015/08/18/020966.short 4100 - http://biorxiv.org/content/early/2015/08/18/020966.full AB - Background Genome assembly remains an unsolved problem. Assembly projects face a range of hurdles that confound assembly. Thus a variety of tools and approaches are needed to improve draft genomes.Results We used a custom assembly workflow to optimize consensus genome map assembly, resulting in an assembly equal to the estimated length of the Tribolium castaneum genome and with an N50 of more than 1 Mb. We used this map for super scaffolding the T. castaneum sequence assembly, more than tripling its N50 with the program Stitch.Conclusions In this article we present software that leverages consensus genome maps assembled from extremely long single molecule maps to increase the contiguity of sequence assemblies. We report the results of applying these tools to validate and improve a 7x Sanger draft of the T. castaneum genome.