Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

By Yong Kong. Genomics, 2011

556 citations recorded by the source corpus.

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/.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a3748e44e1fa723b47b09611f835edae0cfdc586

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Citations in the corpus

FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms (2012, methodology): “CUTADAPT [5] and BTRIM [6] were selected as recently published solutions.”
AdapterRemoval: easy cleaning of next-generation sequencing reads (2012, background): “Btrim Yes Yes Yes Yes No No No Yes Yes [7,8]”
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads (2014, methodology): “Further improvements in Ukkonen’s algorithm by bitwise parallelism were proposed by Myer [5] and implemented in Btrim [6], which has a time complexity of O ( mn / w ) , where w is the word length of the computer; e.g. w equals 64 for a 64-bit machine.”
Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria (2017, methodology): “For processing the sequencing data, raw sequences with perfect matches to barcodes were assigned to different sample libraries and were trimmed using BTRIM with a threshold average quality score higher than 25 over a 5 bp window size and a minimum length of 150 bp (Kong, 2011).”