Bioinformatics_tools

Repository for VERO bioinformatics tools

Contents

metaSNV

Script to parse results from metaSNV analysis and output a count matrix

Usage

To use metaSNV, execute the following command in the command line:

python metaSNV_organizer.py -i "called_SNPs.best_split_*" -s "all_samples.txt" -o "count_matrix.csv"

Command-line Arguments

• -i specifies the input file pattern (e.g., "called_SNPs.best_split_*").
• -s specifies the path to the samples file.
• -o specifies the name of the output file.

DADA2

There are 3 scrpits which can be used to run the DADA2 library on Big Data.

1. For filtering and trimming use script filter.R

Use the following command to run the script

Rscript script.R --forward-path /path/to/FWD --reverse-path /path/to/REV --trunc-len 240 200 --max-ee 2 --trunc-q 11 --max-n 0 --rm-phix TRUE --compress TRUE --verbose TRUE --multithread TRUE

2. To Infer Sequence Variants use script Error.R

Use the following command to run the script

Rscript Error.R --filtered-path /path/to/FWD/filtered --output-path /path/to/run1/output

3. To Merge Runs, Remove Chimeras, Assign Taxonomy

Use the following command to run the script

Rscript Taxonomy.R --run1-seqtab /path/to/run1/output/seqtab.rds --run2-seqtab /path/to/run2/output/seqtab.rds --run3-seqtab /path/to/run3/output/seqtab.rds --taxonomy-file /path/to/silva_nr_v128_train_set.fa.gz --output-path /path/to/study

megares-update

Find new resistance genes in databases, cluster and annotate them, and add them to MEGARes.