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NGS数据分析中的质量控制工具

NGS数据分析中的质量控制工具,老规矩,先占坑!

基本介绍

NGS

  1. QC-Chain (Zhou et al. 2013)1 http://www.computationalbioenergy.org/qc-chain.html
  2. RNA-SeQC (DeLuca et al. 2012)2 https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC
  3. HTQC (Yang et al. 2013)3 http://sourceforge.net/projects/htqc/
  4. Trimmomatic (Lohse et al. 2012)4 http://www.usadellab.org/cms/?page=trimmomatic
  5. NGS QC Toolkit (Patel and Jain 2012)5 http://www.nipgr.res.in/ngsqctoolkit.html
  6. FastUniq (Xu et al. 2012)6 http://sourceforge.net/projects/fastuniq/
  7. RseQC (Wang et al. 2012)7 http://code.google.com/p/rseqc/
  8. CHANCE (Diaz et al. 2012)8 https://github.com/songlab/chance
  9. htSeqTools (Planet et al. 2012)9 http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/htSeqTools.html
  10. DeconSeq (Schmieder and Edwards 2011)10 http://deconseq.sourceforge.net/
  11. ConDeTri (Smeds and Kunstner 2011)11 http://code.google.com/p/condetri/
  12. SAMStat (Lassmann et al. 2011)12 http://samstat.sourceforge.net/
  13. HiTEC (Ilie et al. 2011)13 http://www.csd.uwo.ca/~ilie/HiTEC/
  14. TEQC (Hummel et al. 2011)14 http://sourceforge.net/projects/htqc/
  15. Cutadapt (Martin 2011)15 http://code.google.com/p/cutadapt/
  16. SolexaQA (Cox et al. 2010)16 http://solexaqa.sourceforge.net/
  17. SeqTrim (Falgueras et al. 2010)17 http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext
  18. TagCleaner (Schmieder et al. 2010)18 http://tagcleaner.sourceforge.net/
  19. CANGS (Pandey et al. 2010)19 https://github.com/songlab/chance
  20. NGSQC (Dai et al. 2010) 20 http://brainarray.mbni.med.umich.edu/brainarray/ngsqc/
  21. TagDust (Lassmann et al. 2009)21 http://genome.gsc.riken.jp/osc/english/dataresource/
  22. TileQC (Dolan and Denver 2008)22 http://denverlab.science.oregonstate.edu/tileqc/
  23. SeqClean (Chen et al. 2007)23 http://sourceforge.net/projects/seqclean/files/
  24. PRINSEQ (Morgulis et al. 2006)24 http://prinseq.sourceforge.net/
  25. LUCY/LUCY2 (Li and Chou 2004)25 http://www.complex.iastate.edu/download/Lucy2/
  26. FASTX-Toolkit (Lab Hannon) 26 http://hannonlab.cshl.edu/fastx_toolkit/
  27. Fastq Screen (FastQ Screen Team)27 http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
  28. FastQC (Andrews)28 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  29. Sickle 29 https://github.com/najoshi/sickle
  30. Seqtk 30 https://github.com/lh3/seqtk
  31. scythe 31 https://github.com/vsbuffalo/scythe
  32. qrqc 32 http://bioconductor.org/packages/2.12/bioc/html/qrqc.html
  33. biopieces 33 http://code.google.com/p/biopieces/
  34. SeqQC 34 http://genotypic.co.in/Products/7/Seq-QC.aspx
  35. FLEXBAR (Dodt et al. 2012) 35 http://sourceforge.net/projects/flexbar/
  36. ReQON (Cabanski et al. 2012)36 http://bioconductor.org/packages/2.12/bioc/html/ReQON.html
  37. FreeIbis (Renaud et al. 2013)37 https://github.com/grenaud/freeIbis
  38. RSeQC 38http://sourceforge.net/projects/rseqc/

Reference

  1. Zhou Q, Su X, Wang A, Xu J, Ning K. 2013. QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data. PLoS One 8(4): e60234.

  2. DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G. 2012. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28(11): 1530-1532.

  3. Yang X, Liu D, Liu F, Wu J, Zou J, Xiao X, Zhao F, Zhu B. 2013. HTQC: a fast quality control toolkit for Illumina sequencing data. BMC bioinformatics 14: 33.

  4. Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. 2012. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic acids research 40(Web Server issue): W622-627.

  5. Patel RK, Jain M. 2012. NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data. PLoS One 7(2): e30619.

  6. Xu H, Luo X, Qian J, Pang X, Song J, Qian G, Chen J, Chen S. 2012. FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS One 7(12): e52249.

  7. Wang L, Wang S, Li W. 2012. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28(16): 2184-2185.

  8. Diaz A, Nellore A, Song J. 2012. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biology 13(10): R98.

  9. Planet E, Attolini CS, Reina O, Flores O, Rossell D. 2012. htSeqTools: high-throughput sequencing quality control, processing and visualization in R. Bioinformatics 28(4): 589-590.

  10. Schmieder R, Edwards R. 2011. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 6(3): e17288.

  11. Smeds L, Kunstner A. 2011. ConDeTri–a content dependent read trimmer for Illumina data. PLoS One 6(10): e26314.

  12. -. 2011. SAMStat: monitoring biases in next generation sequencing data. Bioinformatics 27(1): 130-131.

  13. Ilie L, Fazayeli F, Ilie S. 2011. HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 27(3): 295-302.

  14. Hummel M, Bonnin S, Lowy E, Roma G. 2011. TEQC: an R package for quality control in target capture experiments. Bioinformatics 27(9): 1316-1317.

  15. Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal; Vol 17, No 1: Next Generation Sequencing Data Analysis.

  16. Cox M, Peterson D, Biggs P. 2010. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC bioinformatics 11(1): 485.

  17. Falgueras J, Lara AJ, Fernandez-Pozo N, Canton FR, Perez-Trabado G, Claros MG. 2010. SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read. BMC bioinformatics 11: 38.

  18. Schmieder R, Lim YW, Rohwer F, Edwards R. 2010. TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC bioinformatics 11: 341.

  19. Pandey RV, Nolte V, Schlotterer C. 2010. CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. BMC research notes 3: 3.

  20. Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F. 2010. NGSQC: cross-platform quality analysis pipeline for deep sequencing data. BMC Genomics 11 Suppl 4: S7.

  21. Lassmann T, Hayashizaki Y, Daub CO. 2009. TagDust–a program to eliminate artifacts from next generation sequencing data. Bioinformatics 25(21): 2839-2840.

  22. Dolan P, Denver D. 2008. TileQC: A system for tile-based quality control of Solexa data. BMC Bioinformatics 9(1): 250.

  23. Chen YA, Lin CC, Wang CD, Wu HB, Hwang PI. 2007. An optimized procedure greatly improves EST vector contamination removal. BMC Genomics 8: 416.

  24. Morgulis A, Gertz EM, Schaffer AA, Agarwala R. 2006. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 13(5): 1028-1040.

  25. Li S, Chou HH. 2004. LUCY2: an interactive DNA sequence quality trimming and vector removal tool. Bioinformatics 20(16): 2865-2866.

  26. Lab Hannon. FASTX Toolkit.

  27. FastQ Screen Team. Babraham Bioinformatics – FastQ Screen (http://www.bioinformatics.bbsrc.ac.uk/projects/fastq_screen/): NGS reads quality control.

  28. Andrews S. FastQC A Quality Control tool for High Throughput Sequence Data.

  29. https://github.com/najoshi/sickle

  30. https://github.com/lh3/seqtks

  31. https://github.com/vsbuffalo/scythe

  32. http://bioconductor.org/packages/2.12/bioc/html/qrqc.html

  33. http://code.google.com/p/biopieces/

  34. http://genotypic.co.in/Products/7/Seq-QC.aspx

  35. Dodt M, Roehr J, Ahmed R, Dieterich C. 2012. FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology 1(3): 895-905.

  36. Cabanski CR, Cavin K, Bizon C, Wilkerson MD, Parker JS, Wilhelmsen KC, Perou CM, Marron JS, Hayes DN. 2012. ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. BMC bioinformatics 13: 221.

  37. Renaud G, Kircher M, Stenzel U, Kelso J. 2013. freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics.

  38. http://sourceforge.net/projects/rseqc/

update: 2013-08-15

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