ABMapper

The software tool ABMapper is designed to map sequencing reads generated by RNA-sequencing back to the genome through alignment. It is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature, which are not handled well by current fast and memory-saving short-read mappers.

Topic

Mapping;Nucleic acid structure analysis

Detail

  • Operation: Nucleic acid sequence analysis;Prediction and recognition;DNA mapping

  • Software interface: Command-line user interface

  • Language: C++;Perl

  • License: -

  • Cost: Free

  • Version name: 2.0.3_1118

  • Credit: Focused Investment Scheme of the Chinese University of Hong Kong, General Research Fund from the Research Grant Committee, Hong Kong SAR Government.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.
  • Lou SK, et al. ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. 2011; 27:421-2. doi: 10.1093/bioinformatics/btq656
  • https://doi.org/10.1093/bioinformatics/btq656
  • PMID: 21169377
  • PMC: PMC3031031

Download and documentation

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