@@ -16,6 +16,18 @@ Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-
While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Performance
-----------
As of version 2.18, ``bedtools`` is substantially more scalable thanks to improvements we have made in the algorithm used to process datasets that are pre-sorted
by chromosome and start position. As you can see in the plots below, the speed and memory consumption scale nicely
with sorted data as compared to the poor scaling for unsorted data. The current version of bedtools intersect is as fast as (or slightly faster) than the ``bedops`` package's ``bedmap`` which uses a similar algorithm for sorted data. The plots below represent counting the number of intersecting alignments from exome capture BAM files against CCDS exons.
The alignments have been converted to BED to facilitate comparisons to ``bedops``. We compare to the bedmap ``--ec`` option because similar error checking is enforced by ``bedtools``.
