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2.0.2 Assembly of Musca domestica
 A total of 6 female individual DNA isolates were provided in TE buffer for house fly Musca domestica courtesy of Dr. Jeffery Scott. The sequencing plan followed the recommendations provided in the ALLPATHS-LG assembler ... manual. This model requires 45x sequence coverage each of short inserts (overlapping paired reads 
180bp length) and 3kb paired end (PE) reads as well as 5x coverage of 8kb PE reads. For fragments we used DNA sample MDAB-9-14174 and for all jumping libraries (3 and 8kb) we used a pool of these DNA samples MDAB-group40-40, MDAB-group43-43, MDAB-group44-44, MDAB-group47-47 and MDAB-group48-48. We achieved 35x, 27x and 2x sequence coverage for short inserts, 3 and 8kb reads, respectively. PyGap, a post-assembly gap closing program, was run to improve contiguity. The assembly was also screened for contamination, which consisted mostly of human and bacterial contaminants. Trimmed vector in the form of X's and ambiguous bases as N's in the sequence were removed. NCBI requires that all contigs 200bp and smaller be removed. Removing these contigs was the final step in preparation for submitting the 2.0.2 assembly to NCBI.

 Various assembly metrics are summarized here:
 *** Contiguity: Contig *** Total contig number: 104054 Total contig bases: 691739271 bp (genome size, minus gaps) Average contig length: 6648 bp Maximum contig length: 300103 bp N50 contig length: 11807 bp N50 contig number: 14930
 *** Contiguity: Supercontig *** Total supercontig number: 20487 Average supercontig length: 33765 bp Maximum supercontig length: 2295392 bp N50 supercontig length: 213348 bp N50 supercontig number: 786
 ***Scaffold/Supercontigs Distribution*** Scaffolds > 1M: 35 Scaffold 250K--1M: 604 Scaffold 100K--250K: 1082 Scaffold 10--100K: 4640 Scaffold 5--10K: 2584 Scaffold 2--5K: 6000 Scaffold 0--2K: 5542
The VEuPathDB Bioinformatics Resource Center (www.veupathdb.org) may also have contributed to the annotation of this genome. Annotation and related data can be viewed and updated at http://veupathdb.org and inquiries can be sent to help@veupathdb.org.  more

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