gSearch

The software tool 'gSearch' is a multi-threaded search utility that compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. It readily accepts public or user-prepared reference files in various formats including GVF, GFF3, GTF, VCF and BED format. It runs more than 10 times faster than existing tools such as ANNOVAR and is capable of annotating 52.8 million variants with allele frequencies in 6 minutes.

Topic

Whole genome sequencing;Data management

Detail

  • Operation: Sequence database search

  • Software interface: Command-line user interface

  • Language: -

  • License: -

  • Cost: Free for users from academic institutions/non-profit organizations. All commercial users are required to purchase a license.

  • Version name: -

  • Credit: NIH-NHGRI, NIH-NIMH, the Soongsil University Research Fund, the Proteogenomic Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science, and Technology.

  • Input: GVF, GFF3, GTF, VCF and BED format.

  • Output: -

  • Contact: kbhwang@ssu.ac.kr;tmsong@ml.ssu.ac.kr

  • Collection: -

  • Maturity: -

Publications

  • gSearch: a fast and flexible general search tool for whole-genome sequencing.
  • Song T, et al. gSearch: a fast and flexible general search tool for whole-genome sequencing. gSearch: a fast and flexible general search tool for whole-genome sequencing. 2012; 28:2176-7. doi: 10.1093/bioinformatics/bts358
  • https://doi.org/10.1093/bioinformatics/bts358
  • PMID: 22730434
  • PMC: PMC3413394

Download and documentation

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