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RMAP

Reads maps from next-generation sequencing (NGS) technology. RMAP was developed for mapping Illumina reads and has been used to map Roche/454 and ABI SOLiD reads. The software reads map with or without error probability information. It supports paired-end reads either as read sequences or using full quality-score information. RMAP performance was profiled using data from resequencing bacterial artificial chromosomes (BACs) with well-known genomic origin (hg18).

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RMAP classification

RMAP specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTA,FASTQ,(FASTA+PRB)
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://www.cmb.usc.edu/people/andrewds/rmap/rmap_v2.05.tbz2
Interface:
Command line interface
Input data:
Reads files and chromosome files.
Output format:
BED
License:
GNU General Public License version 3.0
Version:
2.05
Requirements:
GCC
Maintained:
Yes

RMAP distribution

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No versioning.

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RMAP support

Documentation

Maintainers

  • Andrew Smith <>
  • Michael Zhang <>
  • Wen-Yu Chung <>

Additional information

Previous version: http://rulai.cshl.edu/rmap/rmap1-webpage/index.shtml

Credits

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Publications

Institution(s)

Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

Funding source(s)

Supported by National Institutes of Health (U01 ES017166 and T32 CA00917631), Department of the
Army (W81XWH04-1-0477), The Breast Cancer Research Foundation and Howard Hughes Medical Institute.

Link to literature

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