HISEA

HISEA is a pairwise read aligner designed for SMRT (Single Molecule, Real-Time) sequencing data. It is used for genome assembly and is specifically designed to detect alignments between reads, a challenging task due to high error rates and long read lengths. HISEA uses a novel two-step k-mer search, employing consistent clustering, k-mer filtering, and read alignment extension. HISEA's sensitivity for detecting alignments is significantly higher than the current best programs for SMRT data, and it has been incorporated into the Canu pipeline for genome assembly.

Topic

Sequence analysis

Detail

  • Operation: Genome assembly

  • Software interface: Command-line user interface

  • Language: Java

  • License: Other

  • Cost: Free

  • Version name: -

  • Credit: Discovery Grant and a Research Tools and Instruments Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC), Ontario Graduate Scholarship (OGS) in Science and Technology.

  • Input: -

  • Output: -

  • Contact: ilie@uwo.ca

  • Collection: -

  • Maturity: -

Publications

Download and documentation

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