title: Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool.
abstract: 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.
authors.affiliation: KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA. sheltonj@ksu.edu.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Shelton
authors.affiliation: KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA. cmgordon@ksu.edu.
authors.forename: Michelle C
authors.initials: MC
authors.lastname: Coleman
authors.affiliation: KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA. nherndon@ksu.edu.
authors.forename: Nic
authors.initials: N
authors.lastname: Herndon
authors.affiliation: BioNano Genomics, San Diego, CA, USA. nanyan@ksu.edu.
authors.forename: Nanyan
authors.initials: N
authors.lastname: Lu
authors.affiliation: BioNano Genomics, San Diego, CA, USA. Elam@bionanogenomics.com.
authors.forename: Ernest T
authors.initials: ET
authors.lastname: Lam
authors.affiliation: BioNano Genomics, San Diego, CA, USA. tanantharaman@bionanogenomics.com.
authors.forename: Thomas
authors.initials: T
authors.lastname: Anantharaman
authors.affiliation: KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA. psheth@bionanogenomics.com.
authors.forename: Palak
authors.initials: P
authors.lastname: Sheth
authors.affiliation: KSU/K-INBRE Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, USA. sjbrown@ksu.edu.
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Brown
mesh_terms: D000818:Animals; D016678:Genome; D023281:Genomics / Q000379:methods; D017422:Sequence Analysis, DNA; D012984:Software; D014231:Tribolium / Q000235:genetics*