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

Summary

Tripal data table
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
Authors	Shelton JM, Coleman MC, Herndon N, Lu N, Lam ET, Anantharaman T, Sheth P, Brown SJ

Cross Reference

Database Reference Annotations

Tripal data table
Database	Accession
PMID	26416786

Analyses

Tripal data table
Name	Program	Status Sort descending
Tribolium castaneum genome assembly Tcas5.2 (GCF_000002335.3)	AllPaths v. 2008; ATLAS-LINK v. 2014; GapFiller v. 2014; stitch v. 2014	Supressed