title: Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia. mail@gtamazian.com.
authors.forename: Gaik
authors.identifier: 0000-0002-2931-1123
authors.initials: G
authors.lastname: Tamazian
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia.
authors.forename: Pavel
authors.initials: P
authors.lastname: Dobrynin
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia.
authors.forename: Ksenia
authors.initials: K
authors.lastname: Krasheninnikova
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Komissarov
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia.|National Zoology Park, Smithsonian Conservation Biology Institute, 3001 Connecticut Avenue NW, Washington, 20008, D.C., USA.
authors.forename: Klaus-Peter
authors.initials: KP
authors.lastname: Koepfli
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Sredniy Prospekt 41A, St. Petersburg, 199004, Russia.|Oceanographic Center, Nova Southeastern University, 8000 N. Ocean Drive, Ft. Lauderdave, 33004, Florida, USA.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D020451:Contig Mapping / Q000379:methods*; D016678:Genome; D016415:Sequence Alignment; D012984:Software
keywords: Alignment; Chromosome assembly; Reference-assisted assembly