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Data released on August 18, 2016

Supporting data for "Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences"

Dobrynin, P; Koepfli, K; Komissarov, A; Krasheninnikova, K; OBrien, S, J; Tamazian, G (2016): Supporting data for "Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences" GigaScience Database. RIS BibTeX Text

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.

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Read the peer-reviewed publication(s):

Tamazian, G., Dobrynin, P., Krasheninnikova, K., Komissarov, A., Koepfli, K.-P., & O’Brien, S. J. (2016). Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences. GigaScience, 5(1). doi:10.1186/s13742-016-0141-6

Additional information:


reference-assisted assembly chromosome assembly alignment 

Software, Genomic


Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
B. taurus9913bovinecattleBos taurus Alternative accession-GenBank:GCF_000003055.5
Assembly name:UMD3.1
E.coli_K-12511145E.coli Alternative accession-RefSeq:NC_000913.3
E.coli_Sakai386585Escherichia coli O157:H7 str. Sakai Alternative accession-SRA Sample:SRR530851, SRR587217
H. sapiens9606HumanhumanHomo sapiens Assembly name:GRCh38.p2
P. hodgsonii59538Tibetan antelopechiruPantholops hodgsonii Alternative accession-GenBank:GCA 000400835.1
P. troglodytes9598 chimpanzeePan troglodytes Alternative accession-GenBank:GCA 000001515.4
S. cerevisiae CLIB324929629Saccharomyces cerevisiae CLIB324Saccharomyces cerevisiae CLIB324 Alternative accession-GenBank:GCA 000192495.1
S. cerevisiae S288c559292  Saccharomyces cerevisiae S288c Alternative accession-GenBank:GCF_000146045.2
Displaying 1-8 of 8 Sample(s).

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
FASTAFASTA128 KB2016-07-18
FASTAFASTA32 KB2016-07-18
FASTAFASTA576 KB2016-07-18
FASTAFASTA144 KB2016-07-18
GitHub archivearchive32.24 KB2016-07-18
FASTAFASTA5.36 MB2016-07-18
OtherTEXT176 KB2016-07-18
OtherTEXT165.18 KB2016-07-18
ReadmeTEXT1.97 KB2016-07-18
Displaying 1-9 of 9 File(s).



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