gSearch: a fast and flexible general search tool for whole-genome sequencing.
BACKGROUND
Various processes such as annotation and filtering of variants or comparison of variants in different genomes are required in whole-genome or exome analysis pipelines. However, processing different databases and searching among millions of genomic loci is not trivial.


RESULTS
gSearch 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. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner. The proposed method is not a stand-alone annotation tool with its own reference databases. Rather, it is a search utility that readily accepts public or user-prepared reference files in various formats including GVF, Generic Feature Format version 3 (GFF3), Gene Transfer Format (GTF), VCF and Browser Extensible Data (BED) format. Compared to existing tools such as ANNOVAR, gSearch runs more than 10 times faster. For example, it is capable of annotating 52.8 million variants with allele frequencies in 6 min.


BACKGROUND
gSearch is available at http://ml.ssu.ac.kr/gSearch. It can be used as an independent search tool or can easily be integrated to existing pipelines through various programming environments such as Perl, Ruby and Python.
School of Computer Science and Engineering, Soongsil University, Seoul 156-743, South Korea.
Taemin
T
Song
Kyu-Baek
KB
Hwang
Michael
M
Hsing
Kyungjoon
K
Lee
Justin
J
Bohn
Sek Won
SW
Kong
D000465:Algorithms; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D057386:Search Engine; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software