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Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
- Source :
- PLoS Computational Biology; 8/21/2019, Vol. 15 Issue 8, p1-19, 19p, 1 Color Photograph, 2 Charts, 7 Graphs
- Publication Year :
- 2019
-
Abstract
- Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds. Despite its increasing popularity, there are limited open-source tools available. Errors, particularly inversions and fusions across chromosomes, remain higher than alternate scaffolding technologies. We present a novel open-source Hi-C scaffolder that does not require an a priori estimate of chromosome number and minimizes errors by scaffolding with the assistance of an assembly graph. We demonstrate higher accuracy than the state-of-the-art methods across a variety of Hi-C library preparations and input assembly sizes. The Python and C++ code for our method is openly available at . [ABSTRACT FROM AUTHOR]
- Subjects :
- GENE libraries
COMPUTATIONAL biology
CHROMOSOMES
LIFE sciences
GENOMES
Subjects
Details
- Language :
- English
- ISSN :
- 1553734X
- Volume :
- 15
- Issue :
- 8
- Database :
- Complementary Index
- Journal :
- PLoS Computational Biology
- Publication Type :
- Academic Journal
- Accession number :
- 138163091
- Full Text :
- https://doi.org/10.1371/journal.pcbi.1007273