Assembly

From AAAWiki

Comparative Assembly Freeze 1 (CAF1) of all 12 genomes is now available for download here.

Assemblies of D. erecta, D. ananassae, D. mojavensis, D. virilis, D. grimshawi and D. willistoni are reconciliations of independent assemblies performed using Arachne and the Celera Assembler. The reconciliations were carried out by Aleksey Zimin and James Yorke at the University of Maryland. Information is available on the Assembly Reconciliation process. The assembly of D. simulans is the "mosaic" assembly and was downloaded from Washington University. Assemblies of D. persimilis and D. sechellia were performed with Arachne and downloaded directly from the Broad Institute. The assembly of D. melanogaster is the published release 4 from the BDGP. There are two versions of assemblies for D. yakuba and D. pseudoobscura. The official CAF1 assemblies are the manually curated assemblies from the genome centers (freeze 2.0 for D. pseudoobscura from BHGC, and DroYak2.1 for D. yakuba from Washington University ), and there are also reconciled versions of each of these assemblies (reconciled against Arachne/Celera assemblies). These assemblies are very similar, but differ subtly and we would like one of the targets of the first round of analyses to compare these assemblies. The reconciliation process has clearly improved areas of each assembly, but may have altered some manually curated regions.