Metassembler: merging and optimizing de novo genome assemblies

Wences, A. H., Schatz, M. C. (September 2015) Metassembler: merging and optimizing de novo genome assemblies. Genome Biol, 16 (1). p. 207. ISSN 1474-760X (Electronic)1474-7596 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/26403281
DOI: 10.1186/s13059-015-0764-4

Abstract

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for meta-assembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source at http://metassembler.sourceforge.net .

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics
bioinformatics > computational biology
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > de novo assembly
bioinformatics > genomics and proteomics > analysis and processing > reference assembly
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: Matt Covey
Date: 24 September 2015
Date Deposited: 02 Oct 2015 15:19
Last Modified: 20 Oct 2015 20:08
PMCID: PMC4581417
Related URLs:
URI: http://repository.cshl.edu/id/eprint/31893

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