To rerun the supplementary scripts with different parameter, please clone this repository and open the .rnw files with Rstudio.
Supplementary materials (Available at https://github.com/adrientaudiere/FEF_paper): FIG S1 (pdf): Bioinformatics pipeline. Available at: https://github.com/adrientaudiere/FEF_paper/blob/master/S1.pdf
SM S2 (markdown and pdf): UNIX scripts for bioinformatics pipeline. Available at: https://github.com/adrientaudiere/FEF_paper/blob/master/S2.Rmd and https://github.com/adrientaudiere/FEF_paper/blob/master/S2.pdf
SM S3 (pdf and associated rnw): Ecological analysis of the Uparse dataset discarding unique sequences in the Bio-informatic pipeline. Available at: https://github.com/adrientaudiere/FEF_paper/blob/master/S3.pdf
SM S4 (pdf and associated rnw): Ecological analysis of the Uparse dataset discarding unique sequences in the Bio-informatic pipeline but keeping sequences putatively assigned to “Tracheophyta” by ITSx. Available at: https://github.com/adrientaudiere/FEF_paper/blob/master/S4.pdf
SM S5 (pdf and associated rnw): Ecological analysis of the Uparse dataset allowing unique sequences in the Bio-informatic pipeline. Available at:https://github.com/adrientaudiere/FEF_paper/blob/master/S5.pdf
SM S6 (pdf and associated rnw): Ecological analysis of the Swarm dataset. Available at: https://github.com/adrientaudiere/FEF_paper/blob/master/S6.pdf
SM S7 (pdf and associated rnw): Ecological analysis of the Open Ref dataset. Available at: https://github.com/adrientaudiere/FEF_paper/blob/master/S7.pdf
SM S8 (pdf and associated rnw): Ecological analysis of the Closed Ref dataset. Available at: https://github.com/adrientaudiere/FEF_paper/blob/master/S8.pdf
FIG S9 (html): Comparison of four taxonomic assignation methods (RDP, Blast, Mothur and Uclust). We build this figure using Krona (Ondov et al. 2011). Available at: http://htmlpreview.github.io/?https://github.com/adrientaudiere/FEF_paper/blob/master/S9.html
FIG S10 (html): FastQC result of sequences quality before quality filtering. Available to download: http://htmlpreview.github.io/?https://github.com/adrientaudiere/FEF_paper/blob/master/S10.html
FIG S11 (html): FastQC result of sequences quality after quality filtering. Available to download: http://htmlpreview.github.io/?https://github.com/adrientaudiere/FEF_paper/blob/master/S11.html