KGGSeq: A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data

Links of MX Li's tools:


KGGSeq is a software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits. Simply, KGGSeq is like a fishing rod facilitating geneticists to fish the genetic determinants of human diseases/traits in the big sea of DNA sequences. Compared with other genetic tools like plink/seq, KGGSeq paid more attention downstream analysis of genetic mapping. Currently, a comprehensive and efficient framework was newly implemented on KGGSeq to filter and prioritize genetic variants from whole exome sequencing data.

KGGSeq V1.0+ has been released! Donwload it! and See Online Manual

Important new features of KGGSeq v1.0+ you may be interested in:

1. Improved capacity to process whole genome sequencing data of large sample IN PARALLEL with REASONABLE AMOUNT of memory, say, < 10GB;
2. Pathogenic prediction for complex diseases at genes and non-coding variants;
3. Statistic tests for mutation rate and association at genes;
4. All in all, it is a comprehensive unified framework for high-throughput sequencing study of human traits, from quality control, filtering, annotation and statistic test.

Comments and suggestions are welcome, please e-mail
  1.  Li et al.Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework. Nucleic Acids Res. 2017 Jan 23. pii: gkx019. doi: 10.1093/nar/gkx019 PubMed ‹For the new version of KGGSeq since version 1.0›
  2.  Li MX, Gui HS, Kwan JS, Bao SY, Sham PC. A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.Nucleic Acids Res. 2012 Apr;40(7):e53. PubMed

The pipeline of KGGSeq V1.0+ :

Miao-xin Li, Center for Genomic Sciences & Department of Psychiatry, The University of Hong Kong, All rights reserved.