# id: 'tools'
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# section_name: 'Tool description'
# description: 'This section describes the tools used during the analysis and their reference'
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#     id: 'tools-plot'
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#     Reference:
#         title: 'Reference'

Tool version	Reference
FastQC v0.11.5	Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
STAR_2.5.2b	Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub  2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905
skewer version: 0.2.2	Jiang H, Lei R, Ding SW, Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182. PubMed PMID: 24925680; PubMed Central PMCID: PMC4074385
QualiMap v.2.2.1	García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics. 2012 Oct 15;28(20):2678-9. doi: 10.1093/bioinformatics/bts503. Epub 2012 Aug 22. PubMed PMID: 22914218
riboPicker version 0.4.3	Schmieder R, Lim YW, Edwards R. Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics. 2012 Feb 1;28(3):433-5. doi: 10.1093/bioinformatics/btr669. Epub 2011 Dec 6. PubMed PMID: 22155869; PubMed Central PMCID: PMC3268242
bedtools v2.25.0	Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824
samtools 1.3.1	Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002