title: Debug013_aegypti_Bundibugyo_Uganda_37
design: As part of an ongoing 1200 Aedes aegypti genomes project, we extracted gDNA from  480 field-collected mosquitoes using the Chemagic DNA tissue protocol and sequenced them to 15x coverage with PE 151bp reads using the Illumina HiSeqX platform. We used three iterative mapping steps to construct an updated African reference based on data from a geographically distributed (Africa only) set of 100 unrelated male mosquitoes. We mapped reads using BWA-MEM. After mapping, we realigned reads near insertions and deletions to improve variant discovery in these regions using GATK IndelRealigner.
library_name: Debug013_aegypti_Bundibugyo_Uganda_37