Misc scripts

Match and Symlink script

This script is used to match specific files in a directory and create symbolic links of the matched files to another directory. Handy if you have to symlink specific files in a directory with many other files.

Usage:

Rscript match_and_symlink.R file_list file_dir output_dir pattern 
recursive_setting

• file_list: A list of file names to match, tab separated file without a header.

• file_dir: The directory of the files in file_list.

• output_dir: The directory where the symlinked files will be placed.

• pattern: The pattern to look for, f. ex. "fastq.gz" or "zip".

• recursive_setting: TRUE/FALSE, specifies if the script should look for files in sub-folders.

Fastqc analysis script

R script for analysis of fastqc reports. The script relies on the .zip files created by fastqc, and use the fastqcr package (https://CRAN.R-project.org/package=fastqcr) for importing the data (no need to unpack the .zip files).

The script creates a few informative plots based on the data from fastqc and saves it in a new folder called "fastqc_results_TODAYS_DATE" in the output_dir location.

Usage:

Rscript fastqc_analysis.R zipfiles_location output_dir

Mash screen analysis script

Script for visualizing and identifying contaminants in read files, based on results from Mash screen. The script creates three files in the specified output directory: One plot and two text files.

Usage:

Rscript mash_screen.R report_dir file_pattern filter_value organism output_dir

• report_dir: Full path to the directory of the mash screen reports

• file_pattern: Suffix of mash screen reports (ex. .out, _out, etc.)

• filter_value: A value set for filtering out results below given value, based on shared hashes. Value between 0-1.

• organism: name of the organism of interest, for example "escherichia coli". Include quotation marks if two words are used. This organism is presumed to be the "wanted" organism in the files.

• output_dir: The directory where the output files are deposited.

Output files:

• contaminated_samples_report.txt: A tab separated text file containing the samples with possible contamination. These are filtered out based on the presence of Identity values above 0.95 other than the organism of interest.

• full_mash_report.txt: A tab separated text file containing the mash screen results where shared hashes were 100/1000 or higher.

• mash_plot.svg: A dotplot that visualizes the results from the mash screen analysis. A cut-off value for the identity value is presented as a horizontal line, where all dots above this line should optimally be of the organism of interest. If not, significant contamination is likely.

Extract gene sequences script

Script for extracting nucleotide or amino acid sequences from multiple .ffn or .faa files created by prokka. Outputs a fasta file with the gene sequences.

Usage:

Rscript extract_gene.R fasta_file_location gene_name nt_or_aa output_dir

• fasta_file_location: The folder where the prokka results are located
• gene_name: Name of the gene, as listed in the .faa or .ffn fasta headers
• nt_or_aa: Either "aa" for amino acid sequences or "nt" for nucleotide sequences
• output_dir: Location of output file

Create manifest files for ENA submission

Script for creating separate manifest files for each sample, used in ENA submission of fastq files. Input is a list over all fastq file names in the submission.

Usage:

Rscript create_manifest_file.R list_file output_dir study name instrument library_name library_source library_selection description

See https://ena-docs.readthedocs.io/en/latest/reads/webin-cli.html for details on values.