Team leader: Hanchen Zheng, Chang Yu
Our group takes full effort to develop standard bioinformatics protocol and pipelines for all kinds of projects related to resequencing. The members work on a wide range of items from alignment program, genetic variant identification as well as implementation of algorithms in population genomics, association studies, comparative genomics and other researches guided by reference DNA sequences.
1) Yanhuang: the first diploid Asian genome
The project sequenced a Han Chinese genome using the Now-Gen sequencing technology. Despite its impact on science, during the project we have developed solutions to sequence a human genome using short reads and identify single nucleotide polymorphisms, insertions/deletions and structural variations involved segmental changes.
2) International 1000 genomes project (participating)
The International 1000 genome project was announced by Sanger Institute in UK, BGI at Shenzhen in China and NHGRI in US at Jan 22, 2008. We participate in developing utilities and general data analysis of the great project. The project will provide a deep catalog of human genomic variants, facilitating medical studies and evolution researches.
3) Resequencing utilities
SOAP: short oligonucleotide alignment program, was developed by Dr. Ruiqiang Li et al. We are working to develop a folds faster new program
SOAP2 based on new data structure and implementations.
SoapSNP, SoapIndel, SoapSV: utilities to build consensus sequence and call variants from alignment result of SOAP.
SoapSOLiD: color-space short oligonucleotide alignment program for SOLiD sequencing
SoapSNP(Population version): utilities to deal with population resequencing data to call consensus and identify genetic variants.