Segemehl
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Application data |
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| Created by | Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia Sharma, Joerg Vogel, Philipp Khaitovitch, Peter F. Stadler & Joerg Hackermueller |
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| Biological application domain(s) | Genomics |
| Principal bioinformatics method(s) | Mapping |
| Created at | Professur für Bioinformatik, Institut für Informatik Universität Leipzig |
| Maintained? | Maybe |
| Input format(s) | FASTA |
| Output format(s) | plain text mapping list, multiple hits per read (if found), unknown standard (if any) |
| Software features | fast, precise, low cost for high-error matching |
| Programming language(s) | C, C++ |
Summary: Map short reads to known genome with tolerance for mismatches and indels using suffix arrays for high accuracy matching
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segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).
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