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 validat

SUBMITTER: Shelton JM 

PROVIDER: S-EPMC4587741 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature