Dear all, I would like to introduce you to the new HaploMerger2 package.
Now it comes with a new and more advanced pipeline which can:
0. be 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 or even achieve better continuity;
5. detect and remove tandem mis-assemblies from haploid 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.
Please feel free to try.
Download site: http://mosas.sysu.edu.cn/genome/download_softwares.php#