Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies - PubMed (original) (raw)
Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
Yong Kong. Genomics. 2011 Aug.
Free article
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/.
Copyright © 2011 Elsevier Inc. All rights reserved.
Similar articles
- AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
Criscuolo A, Brisse S. Criscuolo A, et al. Genomics. 2013 Nov-Dec;102(5-6):500-6. doi: 10.1016/j.ygeno.2013.07.011. Epub 2013 Aug 1. Genomics. 2013. PMID: 23912058 - Optimal spliced alignments of short sequence reads.
De Bona F, Ossowski S, Schneeberger K, Rätsch G. De Bona F, et al. Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300. Bioinformatics. 2008. PMID: 18689821 - Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
Jiang H, Lei R, Ding SW, Zhu S. Jiang H, et al. BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182. BMC Bioinformatics. 2014. PMID: 24925680 Free PMC article. - Alignment of Next-Generation Sequencing Reads.
Reinert K, Langmead B, Weese D, Evers DJ. Reinert K, et al. Annu Rev Genomics Hum Genet. 2015;16:133-51. doi: 10.1146/annurev-genom-090413-025358. Epub 2015 May 4. Annu Rev Genomics Hum Genet. 2015. PMID: 25939052 Review. - Evaluation of next-generation sequencing software in mapping and assembly.
Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ. Bao S, et al. J Hum Genet. 2011 Jun;56(6):406-14. doi: 10.1038/jhg.2011.43. Epub 2011 Apr 28. J Hum Genet. 2011. PMID: 21525877 Review.
Cited by
- Exome sequencing of 75 individuals from multiply affected coeliac families and large scale resequencing follow up.
Mistry V, Bockett NA, Levine AP, Mirza MM, Hunt KA, Ciclitira PJ, Hummerich H, Neuhausen SL, Simpson MA, Plagnol V, van Heel DA. Mistry V, et al. PLoS One. 2015 Jan 30;10(1):e0116845. doi: 10.1371/journal.pone.0116845. eCollection 2015. PLoS One. 2015. PMID: 25635822 Free PMC article. - Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing.
Devran Z, Kahveci E, Özkaynak E, Studholme DJ, Tör M. Devran Z, et al. Mol Breed. 2015;35(4):101. doi: 10.1007/s11032-015-0294-5. Epub 2015 Mar 17. Mol Breed. 2015. PMID: 25798050 Free PMC article. - Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow.
Buschmann D, Haberberger A, Kirchner B, Spornraft M, Riedmaier I, Schelling G, Pfaffl MW. Buschmann D, et al. Nucleic Acids Res. 2016 Jul 27;44(13):5995-6018. doi: 10.1093/nar/gkw545. Epub 2016 Jun 17. Nucleic Acids Res. 2016. PMID: 27317696 Free PMC article. - Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling.
Christopher KJ, Wang B, Kong Y, Weatherbee SD. Christopher KJ, et al. Dev Biol. 2012 Aug 15;368(2):382-92. doi: 10.1016/j.ydbio.2012.06.008. Epub 2012 Jun 12. Dev Biol. 2012. PMID: 22698544 Free PMC article. - Genome-wide scan for selection signatures and genes related to heat tolerance in domestic chickens in the tropical and temperate regions in Asia.
Guo X, Xing CH, Wei W, Zhang XF, Wei ZY, Ren LL, Jiang JJ, Li M, Wang JX, He XX, Wang MS, Jiang RS. Guo X, et al. Poult Sci. 2022 Jul;101(7):101821. doi: 10.1016/j.psj.2022.101821. Epub 2022 Mar 7. Poult Sci. 2022. PMID: 35537342 Free PMC article.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources