bioinfo.starter

Installation

Possible local requirements

Some tools need to be installed locally before running the pipeline for some functions (not all are mandatory, depending on your analysis):

• Probably neccessary for most analysis:

  • cutadapt
  • vsearch

• May be necessary depending on your analysis:

  • fastqc is installed automatically with fastqcr::fastqc_install()
  • blastn
  • mumu
  • multiqc (pip install multiqc)
  • swarm
  • falco

MiscMetabar functions can test for the presence of some of this tools (MiscMetabar::is_cutadapt_installed(), MiscMetabar::is_vsearch_installed(), ...).

Clone from github

git clone git@github.com:adrientaudiere/bioinfo.starter.git name_analyse
cd name_analyse
git checkout -b name_analyse

Adapt to your pipeline

• Replace data/data_raw/metadata/sam_data.csv with good metadata file.
  • Must be a true comma separated csv. If you prefer tabulation or ; you may want to add parameter to function sam_data_matching_names().
  • The name of the file and the the column names indicating the samples are defined at the start of the _targets.R 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
• Modify, add, supress the analysis quarto reports (*.qmd)

Install mumu if you want to use mumu_pq

git clone https://github.com/frederic-mahe/mumu.git
cd ./mumu/
make
make check
make install  # as root or sudo

Install R packages and run targets pipeline

install.packages("pak")
pak::local_install_deps(dependencies = TRUE)
fastqcr::fastqc_install() # install fastqc for UNIX system (Linux and macOS)

if (!require("devtools", quietly = TRUE)) {
  install.packages("devtools")
}
devtools::install_github("adrientaudiere/greenAlgoR")

targets::tar_make()

Rerun only the website build

Run the entire website build

pak::local_install_deps(dependencies = TRUE)
quarto::quarto_render()

Run only selected reports

quarto::quarto_render(here::here("analysis/01_bioinformatics.qmd"))

Colophon

bioinfo.starter is inspired by:

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