How to deal with a haploid genome?

[nottwy]

Dear developers, I'm interested in "how to group the reads into different haplotype groups and construct assembly graph for each haplotype and generate contigs accordingly" which you said in this link: Tips

I want to know which tool you suggest to finish:

1. group reads into different haplotype;
2. construct assembly graph for each haplotype
3. generate contigs accordingly;

Thanks!

[pb-jchin]

please check http://www.nature.com/nmeth/journal/v13/n12/extref/nmeth.4035-S1.pdf Supplementary Figure 13 to 15 and associated text.

[nottwy]

the titles of Figure 13, 14 and 15 are:

1. summary of the graph reduction from sequence overlaps to contigs
2. summary of the graph reduction from sequence overlaps to contigs
3. summary of the greedy SNP phasing algorithm

They demonstrate some rough rationale how falcon assembles. But I need tools which can achieve the explicit aims that you mentioned in your tips.