BitMapper specifications


Unique identifier OMICS_08939
Name BitMapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Yun Xu

Publication for BitMapper

BitMapper citations


Fast and efficient short read mapping based on a succinct hash index

BMC Bioinformatics
PMCID: 5845352
PMID: 29523083
DOI: 10.1186/s12859-018-2094-5

[…] step of most associated pipelines is the mapping of the generated reads to a reference genome.Read mappers fall into one of the two classes. One class, including FastHASH [], mrsFAST [], RazerS3 [], BitMapper [], and Hobbes [], is referred to as all-mappers. All-mappers attempt to find all mapping locations of each read. The other class, including Bowtie2 [], BWA [], and GEM [], is referred to as […]


Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges

Comput Struct Biotechnol J
PMCID: 5581845
PMID: 28883909
DOI: 10.1016/j.csbj.2017.07.004

[…] er of reads or the number of mappings.Both RazerS3 and Hobbes 2 adopt a banded Myers algorithm  to verify each candidates one by one after filtration. To further investigate fine-grained parallelism, BitMapper  extends the banded Myers algorithm to verify multiple candidates against a read simultaneously by loading several bit vectors into a machine word. Moreover, it has implemented this refined […]

BitMapper institution(s)
Key Laboratory on High Performance Computing, Hefei, China; School of Computer Science, University of Science and Technology of China, Hefei, China; Hefei University of Technology, Hefei, China; Department of Computer Science, University of Missouri-Columbia, Columbia, MO, USA

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