Performance comparison across a high-latency network. Comparison of runtimes across a residential broadband connection. The query times correlate with the amount of data transfered over this slower connection-the histogrammed BigWig results are fastest, followed by the per-read ReadDB results (readdb) followed by the BAM results. The server-side histograms with ReadDB (readdb.histogram) demonstrate the best performance as they combine histogrammed data transmission with the fast ReadDB server. Each method was used to query n randomly chosen 1 kb regions; only a single replicate was run. The readdb. histogram test used server-generated histograms such that the data passed across the network is similar to the BigWig format rather than the per-read format in the bamlocal and readdb tests.
Rolfe and Gifford BMC Bioinformatics 2011 12:278 doi:10.1186/1471-2105-12-278