16s data processing and microbiome analysis

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Tools referred to in SOP

• FASTQC - http://www.bioinformatics.babraham.ac.uk/projects/fastqc
• MultiQC - https://multiqc.info/
• PRINSEQ - http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi
• SolexaQA - http://www.biomedcentral.com/1471-2105/11/485
• PEAR - http://bioinformatics.oxfordjournals.org/content/early/2013/10/18/bioinformatics.btt593.full.pdf
• PANDASeq - http://www.biomedcentral.com/1471-2105/13/31
• FLASH - http://bioinformatics.oxfordjournals.org/content/early/2011/09/07/bioinformatics.btr507.full.pdf
• UCHIME - http://drive5.com/usearch/manual/uchime_algo.html
• ChimeraSlayer - http://nebc.nox.ac.uk/bioinformatics/docs/chimeraslayer.html
• Perseus - http://www.biomedcentral.com/1471-2105/12/38/
• UPARSE - http://www.drive5.com/uparse/
• vsearch = https://github.com/torognes/vsearch
• UCLUST - http://www.drive5.com/uclust/downloads1_2_22q.html
• RDP classifier - http://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/
• RTAX - https://github.com/davidsoergel/rtax
• PyNAST - http://www.ncbi.nlm.nih.gov/pubmed/19914921
• INFERNAL - http://infernal.janelia.org/
• FastTree - http://www.microbesonline.org/fasttree/
• IM-TORNADO - http://sourceforge.net/projects/imtornado/
• Mothur - http://www.mothur.org/
• QIIME - http://qiime.org/
• QIIME2 - https://qiime2.org/
• UNIFRAC - http://bmf.colorado.edu/unifrac/
• R packages
  • phyloseq - http://www.bioconductor.org/packages/release/bioc/html/phyloseq.html
  • ade4 - http://cran.r-project.org/web/packages/ade4/index.html
  • DADA2 - https://benjjneb.github.io/dada2

Databases referred to in SOP

• SILVA - http://www.arb-silva.de/
• Greengenes - http://greengenes.lbl.gov/
• RDP classifier - http://rdp.cme.msu.edu/

Bibliography