Mayetiola destructor whole genome assembly v1

The Mdes_1.0 release was based on the assembly of whole genome shotgun reads with the 454 Newbler assembler (v2.1-PreRelease-5/13/2009). Reads from each Newbler scaffold were grouped with any missing pairs, and reassembled using Phrap in an attempt to close the gaps within the Newbler scaffold. In a second round of gap filling, Illumina reads were mapped to sequences next to the gaps in the Newbler scaffolds. For each gap, the mapped Illumina reads and corresponding mate-pairs were extracted and reassembled using Phrap. The Phrap contigs were used where possible to close small gaps. Then, Sanger BAC end sequences were used to further build the scaffolds. Finally the scaffolds were mapped using BAC end sequences and placed on chromosomes using the FPC map.