Hello Dr Seemann,
In Ray, heterozigosity generates shorter assembly seeds.
However, for the contigs, this is not a problem for heterozigosity in
non-repeats.
If both choices go to the same place, one of them is selected.
When a contig stops extending, usually it is because of low-coverage regions.
If I look at gaps in scaffolds, most of them are like this:
CCAAGGTCTGGGGCACAGGGACTGGGGGTCCTGTGAAACAGGGCTTTTGGCTGGGATGGG
AAGGGAACAACTTCATCATGTGCCTTCCCCCCTAATGGTGCCCCACCATCAAATTCATGC
CTCAAGTGCTGCTGGGCACCAGTGAGGTCAGAATGGGAAAGCCAGGACCCCCTGCACCAT
GTAGCTGGACCCATGTGCCAGCACAGCCCTGCACAGCTCACCTTGGTTTTTTGATGTGTA
GTTTTTAAAATGTGTAGAGAAGAGCTCGGGGGGGGGGGGGGNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNCGGGGGGGGGGGGGGGGTTCAGAGTAATTTCTGCGA
AGTGGCAACAGCAAGGAGCTGGTTTTACTTCTTTCCCAATGCTGATTGCCAGCAGTTGCC
AGAAAAGCAAAGCCAGAAAAGGTGGAGGGGGGAGGAGGGGTTTTCCCTGTGATAATTCGA
TCTTGATTTGTTAAAGCACAACTTTCTACAGCTAATCATTAGAGATCTTTCCAGCCACCG
This one for example has a lot of guanines. Probably phasing problems.
>
>
> Sébastien
> ________________________________________
> De : torsten.seem...@gmail.com [torsten.seem...@gmail.com] de la part de
> Torsten Seemann [torsten.seem...@infotech.monash.edu.au]
> Date d'envoi : 10 août 2011 22:44
> À : Matthew MacManes
> Cc : Sébastien Boisvert; denovoassembler-users@lists.sourceforge.net
> Objet : Re: [Denovoassembler-users] Updates on Assemblathon 2
>
> Any update on the parrot assembly? What is N50? I notice that you're
> reconstructing ~1.7Gb- about .5Gb too much. What do you make if that?
>
> Diploid organism heterozigosity breaks the graph and generates contigs for
> allelle locii.
>
> --
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University,
> AUSTRALIA
>
>
Sébastien Boisvert
http://github.com/sebhtml/ray
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