Abstract
BackgroundAs 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.FindingsWe 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.ConclusionsDespite 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-016-0141-6) contains supplementary material, which is available to authorized users.
Highlights
As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study
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
Summary
As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Chromosomer constructs draft chromosomes based only on alignments between fragments (contigs or scaffolds) to be arranged and a reference genome, thereby improving analytical and annotation opportunities for the index species assembly. The start and end positions of aligned regions in both the fragments and the reference chromosomes are required.
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