RT Journal
A1 Huang, Shengfeng
A1 Chen, Zelin
A1 Huang, Guangrui
A1 Yu, Ting
A1 Yang, Ping
A1 Li, Jie
A1 Fu, Yonggui
A1 Yuan, Shaochun
A1 Chen, Shangwu
A1 Xu, Anlong
T1 HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
JF Genome Research 
JO Genome Research 
YR 2012 
FD August 01 
VO 22 
IS 8 
SP 1581 
OP 1588 
DO 10.1101/gr.133652.111 
UL http://genome.cshlp.org/content/22/8/1581.abstract 
AB Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.