Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

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. 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. 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.

• Publication year

  2015

• Venue

  BMC Genomics

• Publication date

  2015-08-18

• Fields of study

  Biology, Medicine, Materials Science, Computer Science

• Identifiers
  DOI 10.1186/s12864-015-1911-8PMID 26416786PMCID 4587741
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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