genner-lab/rufiji-kilombero-biodiversity

12S eDNA biodiversity survey of the Kilombero and Rufiji rivers # rufiji-kilombero-biodiversity 12S eDNA biodiversity survey of the Kilombero and Rufiji rivers **Metabarcoding bioinformatic scripts and assets** ``` # clone repos git clone github.com cd rufiji-kilombero-biodiversity git clone github.com git clone github.com git clone github.com # restore R libs Rscript -e "renv::restore()" # get data from ncbi #scripts/get-data.sh # assemble fish reference library cd meta-fish-lib mkdir -p reports temp/fasta-temp cp ../temp/ncbi-key.R assets/ncbi-key.R Rscript -e "renv::restore()" cp ../assets/species-table.csv assets/species-table.csv cp ../assets/exclusions.csv assets/exclusions.csv scripts/sequences-download.R -q 2000 -t 3 -e false scripts/references-assemble.R -t 4 -m 12s.taberlet # backup (or copy back) cp assets/reference-library-master.csv.gz assets/reference-library-master-nolocal.csv.gz #cp assets/reference-library-master-nolocal.csv.gz assets/reference-library-master.csv.gz # add local seqs and qc cp ../assets/add-local-reflib.R scripts/add-local-reflib.R scripts/add-local-reflib.R # qc scripts/qc.R -t 4 -v false # get refseq cd ../refseq-reflib mkdir temp references Rscript -e "renv::restore()" scripts/download.sh scripts/extract.R -p tele02 scripts/annotate.R -s 42 -p tele02 # copy across refseq, sample sheet and contam file to the pipeline lib cd .. cp refseq-reflib/references/refseq208-annotated-tele02.csv meta-fish-pipe/assets/refseq208-annotated-tele02.csv cp assets/sequencing-master.csv meta-fish-pipe/assets/sequencing-master.csv cp assets/contaminants-exclude.csv meta-fish-pipe/assets/contaminants-exclude.csv # set up pipeline cd meta-fish-pipe Rscript -e "renv::restore()" scripts/session-info.sh -r assets/refseq208-annotated-tele02.csv -c assets/meta-fish-lib-v259.csv # set up libs scripts/prepare-libraries.sh -p tele02 -l lib1 scripts/p …