ReadDB performance compared to other formats. ReadDB's performance nearly matches that of local BAM or BigWig files on the medium and large datasets. Each method was used to query n randomly chosen regions (of size 1 kb, 10 kb, or 100 kb) and the resulting average query time is shown in milliseconds. The client and server machines were connected by gigabit ethernet. ReadDB and the BAM tests retrieved individual hits; BigWig retrieved a histogram in 10 bp bins as the BigWig format cannot store individual read positions. bamlocal and wiglocal queried files on local disks rather than on a remote server.
Rolfe and Gifford BMC Bioinformatics 2011 12:278 doi:10.1186/1471-2105-12-278