Fast Search of Thousands of Short-Read Sequencing Experiments

We introduce Sequence Bloom Trees, a method for querying thousands of short-read sequencing experiments by sequence 485 times faster than existing approaches. The approach searches large data archives for all experiments that involve a given sequence. We use Sequence Bloom Trees to search 2652 human blood, breast, and brain RNA-seq experiments for all 214,293 known transcripts in under 4 days using less than 239 MB of RAM and a single CPU.