See details in our mSystems paper: https://journals.asm.org/doi/full/10.1128/mSystems.00704-21
Psuedomonas species cannot be distuinguised using 16S gene amplicon sequencing. Instead the rpoD primers
ATYGAAATCGCCAARCG
CGGTTGATKTCCTTGA
can be used to generate rpoD-amplicons, which then can be processed by this pipeline.
git clone https://github.com/mikaells/PseudomonasRPOD
chmod 755 PseudomonasRPOD/bowtier.sh
conda create --name rpoD
conda activate rpoD
conda install -c bioconda samtools bowtie2 parallel fastp
If you get a bowtie error about libtbb when running
bowtie2 -h
then do
conda install tbb=2020.2
The program bowtier.sh takes an input folder (-i) containing demultiplexed paired end files, an output folder (-o) and a database (-d)
Test by
#enter folder
cd PseudomonasRPOD
#run the files in pmix_in using the database in db/rpoD_amp and output in out/
./bowtier.sh -i pmix_in/ -o out -d db/rpoD_amp
The out/ -folder will now contain some temporary files, and importantly, the tables/ folder, in which a long table of how many reads mapped to each species for each fastq-pair. Both the unfiltered tables, and only pairs mapped at bowtie quality above 10 is provided.