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Chromosomer specifications

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Unique identifier OMICS_22185
Name Chromosomer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A fragment.
Output data Some draft chromosome sequences.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.1.4a
Stability Alpha
Requirements
bioformats, pyfaidx, pyvcf
Source code URL https://codeload.github.com/gtamazian/chromosomer/zip/v0.1.4a
Maintained Yes

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Maintainer


  • person_outline Gaik Tamazian <>

Publication for Chromosomer

Chromosomer in publications

 (2)
PMCID: 4859572
PMID: 27152522
DOI: 10.1371/journal.pone.0154722

[…] [] v3.1.0 with ionhammer (option—iontorrent for homopolymer correction) for ion torrent data and with spades v3.6.0 for illumina data. reference-assisted assembly of scaffolds was performed with chromosomer []. the s288c genome (release r64-1-1, downloaded from the saccharomyces genome database []) was used as a reference throughout this work. quality of assemblies was estimated with quast […]

PMCID: 4835728
PMID: 27089831
DOI: 10.1038/srep24501

[…] red and green) using bowtie2 with default parameters in sensitive mode, separately. successfully mapped reads were chained together across gaps less than 30 kb to form pseudo-scaffolds by the b-chromosomer tool (https://github.com/ad3002/b-chromosomer). repeat-masking was performed using the de novo asian arowana repeat database obtained by de novo with repeatscout and with repbase […]

Chromosomer institution(s)
Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; National Zoology Park, Smithsonian Conservation Biology Institute, Washington, WA, USA; Oceanographic Center, Nova Southeastern University, Ft. Lauderdave, FL, USA
Chromosomer funding source(s)
Supported by Russian Ministry of Science (11.G34.31.0068).

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