  Btrim is a fast and lightweight software to trim adapters and low quality
regions in reads from ultra high-throughput next-generation sequencing
machines. It also can reliably identify barcodes and assign the reads to the
original samples. Based on a modified Myers's bit-vector dynamic programming
algorithm, Btrim can handle indels in adapters and barcodes. It removes low
quality regions and trims off adapters at both or either end of the reads. A
typical trimming of 30M reads with two sets of adapter pairs can be done in
about a minute with a small memory footprint. Btrim is a versatile stand-alone
tool that can be used as the first step in virtually all next-generation
sequence analysis pipelines. The program is available at
\url{http://graphics.med.yale.edu/trim/}.
