Cola specifications


Unique identifier OMICS_07742
Name Cola
Alternative name Contiguous optimal local aligner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Manfred Grabherr

Publication for Contiguous optimal local aligner

Cola citation


A universal genomic coordinate translator for comparative genomics

BMC Bioinformatics
PMCID: 4086997
PMID: 24976580
DOI: 10.1186/1471-2105-15-227
call_split See protocol

[…] Detailed alignment of the source sequence is performed using the Cola [] implementation of a banded alignment with gap-affine penalties [,] against the target sub-sequence, which is defined by the offset determined by the rapid alignment. For source intervals of >1 […]

Cola institution(s)
Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

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