Annotated scripts for different bioinformatic tasks used in different projects
Script to process amplicon libraries targeting the 16s of Procariotes. The script is based on the DADA2 tutorial version 1.6 Libraries were generated targeting a region of about 400 bp spanning the V4/V5 domains in 16s using primers 515f and 926r
Script to process amplicon libraries targeting the ITS2 domain (starting in the 5.8s flanking and ending in LSU). The script is based on the DADA2 tutorial for ITS version 1.8 Libraries were generated targeting a fragment of variable size using primers fITS7 and ITS4
Script to process amplicon libraries targeting the 18s of Eukaryota with cercozoa specific primers. The script is based on the DADA2 tutorial version 1.6 Libraries were generated targeting a fragment within the v4 region of 18s using a coctail of primers S616F_Cerco, S616F_Eocer, S963R_Cerco, S947R_Cerco
Example R script to taxonomically annotate operational taxonomic units or amplicon sequence variants with the IDTaxa algorithm. This example uses the Silva 16s database v. 138.1 as a reference for taxonomic annotation.
Bash script that executes an R script remotely by taking advantage of a high performance computer cluster administered throuth SLURM
R script to produce a tvs file to archive runs at ENA the European Nucleotide Database ENA. The script relates the run files with the accession numbers provided by ENA.
Shell commands to archive Illumina run files genereted during a study. The files can be archived at the European Nucleotide Database ENA
Shell commands and loop functions to concatenate files repeated during sequencing