Abstract
Next-generation sequencing technologies are extensively used in many fields of biology. One of the problems, related to the utilization of this kind of data, is the analysis of raw sequence quality and removal (trimming) of low-quality segments while retaining sufficient information for subsequent analyses. Here, we present a series of methods useful for converting and for refinishing one or more sequence files. One of the methods proposed, based on dynamic trimming, as implemented in the software StreamingTrim allows a fast and accurate trimming of sequence files, with low memory requirement.
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References
Pettersson E, Lundeberg J, Ahmadian A (2009) Generations of sequencing technologies. Genomics 93:105–111
Sawicki MP, Samara G, Hurwitz M, Passaro E (1993) Human genome project. Am J Surg 165:258–264
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 8:175–185
Walther D, Bartha G, Morris M (2001) Base calling with lifetrace. Genome Res 11:875–888
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38:1767–1771
Wikipedia (2014) ASCII. Wikipedia, the free encyclopedia
Wikipedia (2014) FASTQ format. Wikipedia, the free encyclopedia
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 72:557–578
Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485
Smeds L, Künstner A (2011) ConDeTri-a content dependent read trimmer for Illumina data. PLoS One 6:e26314
Patel RK, Jain M (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7:e30619
Bacci G, Bazzicalupo M, Benedetti A, Mengoni A (2014) StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies. Mol Ecol Resour 14:426–434
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics 24:2096–2097
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Field D, Tiwari B, Booth T, Houten S, Swan D, Bertrand N, Thurston M (2006) Open software for biologists: from famine to feast. Nat Biotechnol 24:801–804
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Bacci, G. (2015). Raw Sequence Data and Quality Control. In: Mengoni, A., Galardini, M., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 1231. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1720-4_9
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DOI: https://doi.org/10.1007/978-1-4939-1720-4_9
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1719-8
Online ISBN: 978-1-4939-1720-4
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