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ABMapper | A suffix array-based tool for multi-location searching and splice-junction mapping

Maps ab initio sequence reads that span across splicing junctions or reads that have multiple putative locations within the genome. ABMapper is based on a fast suffix-array algorithm and a dual-seed strategy. It can retrieve all putative locations of reads. This tool allows researchers to specify the seed length, in order to play with the searching speed, sensitivity and accuracy. It can tolerate dynamic error and allows overlapping extension exploration.

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ABMapper forum

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ABMapper classification

ABMapper specifications

Unique identifier:
OMICS_01238
Interface:
Command line interface
Input data:
Some reads.
Output data:
The alignment details, junction sites, putative locations of repetitive reads.
Programming languages:
C++, Perl
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Input format:
BWA,SAM,FASTA,FASTQ
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Maintained:
Yes

ABMapper distribution

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No versioning.

ABMapper support

Maintainer

  • Ting-Fung Chan <>

Credits

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Publications

Institution(s)

Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shati, China; School of Life Sciences, The Chinese University of Hong Kong, Shati, China; Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shati, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Shati, China

Funding source(s)

Supported by a Focused Investment Scheme of the Chinese University of Hong Kong; and a General Research Fund (GRF461708) from the Research Grant Committee, Hong Kong SAR Government.

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