Shengfeng Huang, the author of HaploMerger, informed us about the release of HaploMerger2 built with new and improved algorithm. Those working on assembly of heterozygous genomes should give it a try.
Here is the new flowchart of HaploMerger2 -
Shengfeng wrote -
Now it comes with a new pipeline which can:
0. be more efficient, accurate and easier to use;
1. reconstruct the allelic relationships within a diploid assembly;
2. detect and correct mis-joins in a diploid assembly;
3. reconstruct two haploid assemblies for the diploid assembly: the reference and the alternative haploid assemblies;
4. further scaffold a haploid assembly (by using third-party software) to restore and achieve better continuity;
5. detect and remove tandem mis-assemblies from haploid (or so diploid) assemblies;
6. finish N-gaps in haploid assemblies (by using third-party software) to achieve better contiguity;
7. Many new features, improved quality and bug fixing.
Download site: http://mosas.sysu.edu.cn/genome/download_softwares.php
Our previous posts on diploid assembly -