I'm trying to assemble small (20Mb), diploid fungal genome from MiSeq reads (~400bp after merging, 100x coverage).

The tricky thing: it's heterozygous. The divergence is ~4%, but there are hundreds (thousands?) loss of heterozygosity (LOH) regions, accounting in total to almost half of the genome...

Do you know of any assembler (methodology) capable of handling with such data?

I have tried many assemblers/tricks:

 - de Bruijn graph: Velvet, ABySS, SOAPdenovo
 - overlap-based: MIRA, Newbler
 - clustering reads and then assembling with CAP3

but with rather bad effects. Every time, the assembly was very fragmented (N50 ~10kb), homozygous regions (LOH) were collapsed with ~200x, while heterozygous regions were separated with 100x.

I will be happy to hear about any ideas:)

**EDIT**

As no satisfactory solution exists, I'm developing [Redundans][1] (check [below][2] for more info).

 [1]: https://github.com/lpryszcz/redundans
 [2]: https://www.biostars.org/p/63047/#139529
As there were no good solutions, I've developed a tool that assists assembly of heterozygous/hybrid genomes ([Redundans][1]).

The program takes as input **assembled contigs**, **paired-end and/or mate pairs sequencing libraries** and returns **scaffolded homozygous genome assembly**. Resulting assembly should be **less fragmented** and with total **size smaller** than the input contigs. In addition, Redundans will automatically **close the gaps **resulting from genome assembly or scaffolding ([more details][2]).

Hopefully, someone else will benefit from that! I'll be really grateful for your feedback.

BTW: sorry for being necromancer;)

 [1]: https://github.com/lpryszcz/redundans
 [2]: https://github.com/lpryszcz/redundans/blob/master/test#redundans-pipeline