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Title: Accurate detection of chimeric contigs via Bionano optical maps
Abstract Summary

A chimeric contig is contig that has been incorrectly assembled, i.e. a contig that contains one or more mis-joins. The detection of chimeric contigs can be carried out either by aligning assembled contigs to genome-wide maps (e.g. genetic, physical or optical maps) or by mapping sequenced reads to the assembled contigs. Here, we introduce a software tool called Chimericognizer that takes advantage of one or more Bionano Genomics optical maps to accurately detect and correct chimeric contigs. Experimental results show that Chimericognizer is very accurate, and significantly better than the chimeric detection method offered by the Bionano Hybrid Scaffold pipeline. Chimericognizer can also detect and correct chimeric optical molecules.

Availability and implementation

https://github.com/ucrbioinfo/Chimericognizer

Supplementary information

Supplementary data are available at Bioinformatics online.

 
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Award ID(s):
1814359 1543963 1526742
NSF-PAR ID:
10393446
Author(s) / Creator(s):
; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
Bioinformatics
Volume:
35
Issue:
10
ISSN:
1367-4803
Page Range / eLocation ID:
p. 1760-1762
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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