title: Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.
abstract: 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 http://graphics.med.yale.edu/trim/.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT 06510, USA. yong.kong@yale.edu
authors.forename: Yong
authors.initials: Y
authors.lastname: Kong
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software