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Maps large amount of oligonucleotide to the genome. SeqMap allows up to five mixed substitutions and inserted/deleted (indel) nucleotides in the mapping, which is considered. The software also provides many command line options for tuning almost every aspect of the mapping process. By simply splitting the reads or the genome or both into several parts, SeqMap can be used in parallel on large scale data sets to speed up the mapping process.

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SeqMap classification

SeqMap specifications

Software type:
Restrictions to use:
Academic or non-commercial use
Output format:
Programming languages:
Source code URL:
Command line interface
Input format:
FASTA, raw DNA sequence format
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:

SeqMap distribution


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SeqMap support



  • Hui Jiang <>
  • Wing Hung Wong <>


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Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA; Department of Statistics, Stanford University, Stanford, CA, USA

Funding source(s)

National Institute of Health (R01HG003903 and U54GM62119).

Link to literature

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