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

TL;DR

Btrim is a fast, lightweight tool for trimming adapters and low-quality regions from next-generation sequencing reads, capable of handling indels and sample barcodes efficiently.

Contribution

It introduces a novel, efficient algorithm based on Myers's bit-vector dynamic programming for high-speed trimming with indel handling.

Findings

Trims 30 million reads in about a minute

Handles indels in adapters and barcodes reliably

Uses minimal memory and integrates easily into pipelines

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 \url{http://graphics.med.yale.edu/trim/}.