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

Summary
Cross Reference
References
Summary
Publication Type
Journal Article
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.
Citation
Shelton JM, Coleman MC, Herndon N, Lu N, Lam ET, Anantharaman T, Sheth P, Brown SJ. Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool.. BMC genomics. 2015 Sep 29; 16:734.
Publication Date
2015 Sep 29
DOI
10.1186/s12864-015-1911-8
Cross Reference
PMID
References
Analysis