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
Some approaches I'm aware of are gap closing, e.g.
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.