This is a fork of the original HaploMerger2 software.

The aim of this fork is to provide users with a single line bash script to run the basic Haplomerger2 processes, referred to as hm.batchA, hm.batchB and hm.batchD in the original documentation.

Citation

I recommend that you cite the original Haplomerger2 paper if you use this script.

• Shengfeng Huang, et al. HaploMerger2: rebuilding both haploid sub-assemblies from a heterozygous animal diploid genome assembly.

Depending on the soft-masking strategy deployed (see Inputs below), the masking software should also be cited.

Inputs

HaploMerger2 runs optimally on a soft-masked assembly. This should be provided to the script with the option -f. Soft-masking may be performed with any software, Haplomerger2 reccomends WindowMasker, described here Please refer to the Haplomerger2 manual for more information and instructions.

The number of threads may also be specified with -t.

Finally, by default HaploMerger2 and this bash script will only perform the final stage (remove tanem assemblies) on the reference assembly. -a modifies this and will perform the final stages on the alternative assembly as well as the reference assembly.

Other Considerations

The original HaploMerger2 software also provides options to run:

a scaffolding stage with mate-pair reads, using SSPACE a gap-filling stage with paired-end reads using GapCloser

Should users want to make use of these work-flows then the original HaploMerger2 software should be used.

If users want to scaffold or gap-fill with other types of reads (e.g. single molecule), within the workflow, as prescribed by the HaploMerger2 documentation then the original HaploMerger2 workflow should be modified.