TY - JOUR

T1 - Chromosomer

T2 - A reference-based genome arrangement tool for producing draft chromosome sequences

AU - Tamazian, Gaik

AU - Dobrynin, Pavel

AU - Krasheninnikova, Ksenia

AU - Komissarov, Aleksey

AU - Koepfli, Klaus Peter

AU - O'Brien, Stephen J.

N1 - Publisher Copyright: © 2016 The Author(s).

PY - 2016

Y1 - 2016

N2 - Background: As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, reference-assisted assemblies that use comparative inference have become widely used, prompting the development of several reference-assisted assembly programs for prokaryotic and eukaryotic genomes. Findings: We developed Chromosomer - a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that implement common operations accompanying the genome assembly process. Conclusions: Despite implementing a straightforward alignment-based approach, Chromosomer is a useful tool for genomic analysis of species without chromosome maps. Putative chromosome assemblies by Chromosomer can be used in comparative genomic analysis, genomic variation assessment, potential linkage group inference and other kinds of analysis involving contig or scaffold mapping to a high-quality assembly.

AB - Background: As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, reference-assisted assemblies that use comparative inference have become widely used, prompting the development of several reference-assisted assembly programs for prokaryotic and eukaryotic genomes. Findings: We developed Chromosomer - a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that implement common operations accompanying the genome assembly process. Conclusions: Despite implementing a straightforward alignment-based approach, Chromosomer is a useful tool for genomic analysis of species without chromosome maps. Putative chromosome assemblies by Chromosomer can be used in comparative genomic analysis, genomic variation assessment, potential linkage group inference and other kinds of analysis involving contig or scaffold mapping to a high-quality assembly.

KW - Alignment

KW - Chromosome assembly

KW - Reference-assisted assembly

UR - http://www.scopus.com/inward/record.url?scp=85007385179&partnerID=8YFLogxK

U2 - 10.1186/s13742-016-0141-6

DO - 10.1186/s13742-016-0141-6

M3 - Article

C2 - 27549770

AN - SCOPUS:85007385179

VL - 5

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 1

M1 - 38

ER -