cami/ppsp repository overview

⁠PhyloPythiaS+ (Gregor et al. PeerJ 2016, https://github.com/algbioi/ppsp⁠)

⁠How to use this docker image

PhyloPythiaS+ requires a reference database, which can be downloaded from https://osf.io/heksw/⁠. Download and extract all files:

tar xzvf mg5.tar.gz
tar xzvf ncbi_taxonomy.tar.gz
cat refseq93.tar.gz.* | tar xzvf -
cat SILVA_132.tar.gz.* | tar xzvf -

Once the files are extracted, you should have directories mg5, ncbi_taxonomy, refseq93, and SILVA_132.

PhyloPythiaS+ can then be run as follows (adjust paths as needed):

docker run -v /home/username:/host cami/ppsp /opt/run_ppsp.py \
--pipelineDir /host/output \
--inputFastaFile /host/sequences.fasta \
--databaseFile /host/ref_database/ncbi_taxonomy \
--refSeq /host/ref_database/refseq93 \
--s16Database /host/ref_database/SILVA_132 \
--mgDatabase /host/ref_database/mg5

Parameters description:

• pipelineDir: Project pipeline directory for output and temporary data
• inputFastaFile: Fasta file containing contigs/sequences (for the classification)
• databaseFile: Directory that contains file named "ncbitax_sqlite.db" that represents the NCBI taxonomy in the sqlite3 format
• refSeq: Directory containing all reference sequences that can be used to train PhyloPythiaS
• s16Database: Directory containing the "16S" marker gene reference databases (16S, 23S, 5S)
• mgDatabase: Directory containing the "31" marker gene databases