De novo assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

To see the most recent de novo assembly paper, I found this paper(http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000891). I will just focus on genomic assembly part in this paper.


They use solexa and FLX data. They produce a single and two paired-end data of different insert size libraries from solexa and single read from FLX. The amount of data showed in figures. A little bit doubtful point is the amount of read is too small compared with my data. This maybe come from the difference of version of solexa.

assembly process


The assembly process is simple. They assembled the total raw data from both system and contig from FLX data with Velvet. They said that FLX data reduced the gaps in contigs and addition of paired-end data improved N50 size.



confirmation of assembly


Checking the existence of synteny block between draft genome and closed species. Predicted protein from draft genome mapped to relatively closed species.

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

I choose this paper for reporting in full, because 

1. this is published in science (what I feel in these days is that science is the most hard  journal to understand exactly, this means that the paper in this journal compress enormous knowledge, so this make me study a lot),

2. this paper contain de novo assembly, so I want to find how they do that and confirm the assemly,

3. they compare two relative species, 

All of these reasons are the factors that make me feel this paper can be my role model paper.