From gilbertd from net.bio.net  Fri Jul 16 12:13:41 2010
From: gilbertd from net.bio.net (Don Gilbert)
Date: Fri Jul 16 12:14:12 2010
Subject: [Arthropod] Protocol to improve draft bug genomes with Illumina
	reads?
Message-ID: <201007161713.o6GHDfe23750@net.bio.net>


Dear all,

Does anyone have suggestions or experience with improving draft
genome assemblies with new short read dna? We are thinking about
this for the Daphnia pulex assembly, now 4 years old, with a pile
of new 40x Illimina paired end genomic data for several related
populations.

Some approaches I'm aware of are gap closing, e.g.
  http://genomebiology.com/2010/11/4/R41
which looks useful and straightforward, but may not solve
mistakes in the original assembly.  Or a complete new assembly
say with Celera assembler (mixing old Sanger data + new
Illumina), which would be much more work, and give us an assembly
that the old gene data cannot be easily mapped to.  But it might
be much improved if the old one has more mistakes than we'd like.

-- Don

From gilbertd from net.bio.net  Thu Jul 22 11:49:51 2010
From: gilbertd from net.bio.net (Don Gilbert)
Date: Thu Jul 22 11:51:36 2010
Subject: [Arthropod] Re: Protocol to improve draft bug genomes with Illumina
	reads?
Message-ID: <201007221649.o6MGnpV08157@net.bio.net>

Dear all,

I did get a couple of replies to my question: 

Kim Worley at Baylor College of Med. genome center says "We've
worked with combining data in assemblies. Different data and
different assemblers or versions of assemblers work better in
some combinations and worse in others."  They also have
an unpublished tool to scaffold and gap fill with this data.

Scott Emrich has experience in this with insect/arthropod genomes 
n collaboration with the Celera assembler group at U Maryland,
and offered to help us apply this with the Daphnia genome.

There is also this recent summary paper on uses/problems for
genome assembly with second/next generation data.
  Assembly of large genomes using second-generation sequencing 
  Michael C Schatz, Arthur L Delcher and Steven L. Salzberg 
  Genome Res., May 2010  doi:10.1101/gr.101360.109 

-- Don