README.md

bioinfo.starter

The goal of bioinfo.starter is to [...]

Installation

Clone from github

git clone [email protected]:adrientaudiere/bioinfo.starter.git
git checkout -b name_analyse

Adapt to your pipeline

• Replace data/data_raw/metadata/sam_data.csv with good metadata file
• Copy fastq files in data/data_raw/rawseq
• Add references database in data/data_raw/refseq
• Modify the _targets.R files (at least modify primers sequences and name of the reference database)
• Modify (if necessary) params pattern_remove_sam_data and pattern_remove_fastq_files to make matching fastq files and sample names in metadata

Install R packages and run targets pipeline

renv::install()
targets::tar_make()

Colophon

bioinfo.starter is inspired by:

• {rrtools} developed by Ben Marwick et al.
• {rcompendium} developed by Nicolas Casajus.
• The Turing way recommendation