PyroTrimmer: a Software with GUI for Pre-Processing 454 Amplicon Sequences

Jeongsu Oh; Byung Kwon Kim; Wan-Sup Cho; Soon Gyu Hong; Kyung Mo Kim

doi:10.1007/s12275-012-2494-6

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Research Support, Non-U.S. Gov't
PyroTrimmer: a Software with GUI for Pre-Processing 454 Amplicon Sequences: Jeongsu Oh ^1,2, Byung Kwon Kim ³, Wan-Sup Cho ², Soon Gyu Hong ⁴, Kyung Mo Kim ¹; Journal of Microbiology 2012;50(5):766-769.
DOI: https://doi.org/10.1007/s12275-012-2494-6
Published online: November 4, 2012

¹Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea, ²Department of Bio-Information Technology, Chungbuk National University, CheongJu 361-763, Republic of Korea, ³Department of Systems Biology, Yonsei University, Seoul 120-749, Republic of Korea, ⁴Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea

Corresponding author: Kyung Mo Kim , Tel: +82-42-860-4613,

Received: 10 September 2012 • Accepted: 26 September 2012

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Abstract

The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct lowquality sequences. We have developed a program called Pyro-Trimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.

Keywords: 454;pre-processing;pyrosequencing;trimming;software

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PyroTrimmer: a Software with GUI for Pre-Processing 454 Amplicon Sequences

J. Microbiol. 2012;50(5):766-769. Published online November 4, 2012

DOI: https://doi.org/10.1007/s12275-012-2494-6

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