An extensive evaluation of read trimming effects on illumina NGS data analysis

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Del Fabbro, Cristian ^a   Scalabrin, Simone ^b   Morgante, Michele ^a   Giorgi, Federico M ^a,c  

^a Institute of Applied Genomics   (Italy)

^b IGA Technology Services   (Italy)

^c Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE EXPRESSION; GENETIC ALGORITHM; GENOME; GENOTYPE; HIGH THROUGHPUT SEQUENCING; MEDICAL RESEARCH; NEXT GENERATION SEQUENCING; RELIABILITY; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RESEARCH DESIGN;

EID: 84893443187     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085024     Document Type: Article

References (45)

1. Biesecker LG, Burke W, Kohane I, Plon SE, Zimmern R (2012) Next-generation sequencing in the clinic: are we ready? Nat Rev Genet 13: 818-824. doi:10.1038/nrg3357. PubMed: 23076269.
2. Schuster SC (2007) Next-generation sequencing transforms today's biology. Nature 200.
3. Li R, Fan W, Tian G, Zhu H, He L et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317. PubMed: 20010809.
4. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652. doi:10.1038/nbt.1883. PubMed: 21572440.
5. Iyer MK, Chinnaiyan AM, Maher CA (2011) ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics 27: 2903-2904. doi:10.1093/bioinformatics/btr467. PubMed: 21840877.
6. Bansal V, Bafna V (2008) HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24: i153-i159. doi:10.1093/bioinformatics/btn298. PubMed: 18689818.
7. Krueger F, Kreck B, Franke A, Andrews SR (2012) DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9: 145-151. doi:10.1038/nmeth.1828. PubMed: 22290186.
8. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63. doi:10.1038/nrg2484. PubMed: 19015660.
9. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi:10.1093/ bioinformatics/btp324. PubMed: 19451168.
10. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi:10.1186/gb-2009-10-3-r25. PubMed: 19261174.
11. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD et al. (2012) VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22: 568-576. doi:10.1101/gr.129684.111. PubMed: 22300766.
12. Danecek P, Auton A, Abecasis G, Albers CA, Banks E et al. (2011) The variant call format and VCFtools. Bioinformatics 27: 2156-2158. doi:10.1093/bioinformatics/btr330. PubMed: 21653522.
13. 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. doi:10.1093/nar/gkp1137. PubMed: 20015970.
14. Ewing B, Green P (1998) Base-calling of automated sequencer traces usingPhred. II. error probabilities. Genome Res 8: 186-194. PubMed: 9521922. (Pubitemid 28177230)
15. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829. doi:10.1101/gr.074492. 107. PubMed: 18349386. (Pubitemid 351645072)
16. Smeds L, Künstner A (2011) ConDeTri-A Content Dependent Read Trimmer for Illumina Data. PLOS ONE 6: e26314. doi:10.1371/journal.pone.0026314. PubMed: 22039460.
17. Kelley DR, Schatz MC, Salzberg SL (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol 11: R116. doi:10.1186/gb-2010- 11-11-r116. PubMed: 21114842.
18. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108: 1513-1518. doi:10.1073/pnas. 1017351108. PubMed: 21187386.
19. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117-1123. doi:10.1101/gr.089532.108. PubMed: 19251739.
20. Robertson G, Schein J, Chiu R, Corbett R, Field M et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7: 909-912. doi:10.1038/nmeth.1517. PubMed: 20935650.
21. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65. doi:10.1038/nature08821. PubMed: 20203603.
22. Carter SL, Cibulskis K, Helman E, McKenna A, Shen H et al. (2012) Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol 30: 413-421. doi:10.1038/nbt.2203. PubMed: 22544022.
23. Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K et al. (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641. doi:10.1038/nature11119. PubMed: 22660326.
24. Liu S, Li W, Wu Y, Chen C, Lei J (2013) De Novo Transcriptome Assembly in Chili Pepper (Capsicum frutescens) to Identify Genes Involved in the Biosynthesis of Capsaicinoids. PLOS ONE 8: e48156. doi:10.1371/journal.pone. 0048156. PubMed: 23349661.
25. Karlsson FH, Fåk F, Nookaew I, Tremaroli V, Fagerberg B et al. (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun 3: 1245. doi:10.1038/ncomms2266. PubMed: 23212374.
26. Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L et al. (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and crosscomparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res 40: 10084-10097. doi:10.1093/nar/gks804. PubMed: 22965124.
27. Giorgi FM, Del Fabbro C, Licausi F (2013) Comparative study of RNA-seq-and Microarray-derived coexpression networks in Arabidopsis thaliana. Bioinformatics 29: 717-724. doi:10.1093/bioinformatics/btt053. PubMed: 23376351.
28. Schott T, Kondadi PK, Hänninen M-L, Rossi M (2012) Microevolution of a zoonotic Helicobacter population colonizing the stomach of a human host before and after failed treatment. Genome Biol Evol 4: 1310-1315. doi:10.1093/gbe/evs107. PubMed: 23196968.
29. Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11: 485. doi:10.1186/1471-2105-11-485. PubMed: 20875133.
30. Schmieder R, Edwards R (2011) Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLOS ONE 6: e17288. doi:10.1371/journal.pone.0017288. PubMed: 21408061.
31. Pireddu L, Leo S, Zanetti G (2011) SEAL: a distributed short read mapping and duplicate removal tool. Bioinformatics 27: 2159-2160. doi:10.1093/ bioinformatics/btr325. PubMed: 21697132.
32. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EmBnet Journal 17: 10-12.
33. Bio CLC website. Available: http://www.clcbio.com/manual/genomics/ Quality-abif-trimming.html. Accessed 2013 September 26
34. Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE et al. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40: W622-W627. doi:10.1093/nar/gks540. PubMed: 22684630.
35. Leinonen R, Sugawara H, Shumway M (2011) The sequence read archive. Nucleic Acids Res 39: D19-D21. doi:10.1093/nar/gkq768. PubMed: 21062823.
36. Dunham I, Birney E, Lajoie BR, Sanyal A, Dong X et al. (2012) An integrated encyclopedia of DNA elements in the human genome. PubMed: 22955616
37. Verde I, Abbott AG, Scalabrin S, Jung S, Shu S et al. (2013) The highquality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45: 487-494. doi:10.1038/ng.2586. PubMed: 23525075.
38. Halfmann R, Jarosz DF, Jones SK, Chang A, Lancaster AK et al. (2012) Prions are a common mechanism for phenotypic inheritance in wild yeasts. Nature 482: 363-368. doi:10.1038/nature10875. PubMed: 22337056.
39. Brabaham Bioinformatics website. Available: http://www.bioinformatics. babraham.ac.uk/projects/fastqc/. Accessed 2013 Dec 1
40. Trapnell C, Roberts A, Goff L, Pertea G, Kim D et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7: 562-578. doi:10.1038/nprot.2012.016. PubMed: 22383036.
41. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D et al. (2011) The UCSC genome browser database: update 2011. Nucleic Acids Res 39: D876-D882. doi:10.1093/nar/gkq963. PubMed: 20959295.
42. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C et al. (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40: D1202-D1210. doi:10.1093/nar/gkr1090. PubMed: 22140109.
43. Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A (2013) GAMNGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics 14: S6. doi:10.1186/1471-2105-14-S17-A6. PubMed: 23815503.
44. Delcher AL, Salzberg SL, Phillippy AM (2003) Using MUMmer to identify similar regions in large sequence sets. Current Protocols in Bioinformatics: 10.13. 11-10.13. 18
45. Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G et al. (2012) Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res 40: D700-D705. doi:10.1093/nar/gkr1029. PubMed: 22110037.