Package: panta
Pan-genome pipelineInstallationDepencencies:bedtoolsCD-HITBLASTDIAMONDMCLpandasSeqIOThe simplest method is installed via conda:Download and install the appropriate conda, such as miniconda fromhereCreate a conda environment with all the necessary dependencies: From the repository directory runcondacreate-y-cconda-forge-cdefaults--namepantapython=3.10mamba

condaactivatepanta

mambainstall-y-cconda-forge-cbioconda-canaconda-cdefaults--filerequirements.txt

pipinstall.UsageActivate conda enviroment:source activate pantaMain pipeline: run pan-genome analysis for the first timeusage: panta main [-h] [-g [GFF ...]] [-f TSV] -o OUTDIR [-s] [-b {diamond,blast}] [-i IDENTITY] [--LD LD] [--AL AL] [--AS AS] [-e EVALUE]
                          [-t THREADS] [--table TABLE] [-a [{nucleotide,protein} ...]]

Main pipeline: run pan-genome analysis for the first time

options:
  -h, --help            show this help message and exit
  -g [GFF ...], --gff [GFF ...]
                        gff input files (default: None)
  -f TSV, --tsv TSV     tsv input file (default: None)
  -o OUTDIR, --outdir OUTDIR
                        output directory (default: None)
  -s, --dont-split      dont split paralog clusters (default: False)
  -b {diamond,blast}, --blast {diamond,blast}
                        method for all-against-all alignment (default: diamond)
  -i IDENTITY, --identity IDENTITY
                        minimum percentage identity (default: 0.7)
  --LD LD               length difference cutoff between two sequences (default: 0)
  --AL AL               alignment coverage for the longer sequence (default: 0)
  --AS AS               alignment coverage for the shorter sequence (default: 0)
  -e EVALUE, --evalue EVALUE
                        Blast evalue (default: 1e-06)
  -t THREADS, --threads THREADS
                        number of threads to use, 0 for all (default: 0)
  --table TABLE         codon table (default: 11)
  -a [{nucleotide,protein} ...], --alignment [{nucleotide,protein} ...]
                        run alignment for each gene cluster (default: None)Add pipeline: add sample into previous collectionusage: panta add [-h] [-g [GFF ...]] [-f TSV] -c COLLECTION_DIR [-s] [-b {diamond,blast}] [-i IDENTITY] [--LD LD] [--AL AL] [--AS AS]
                         [-e EVALUE] [-t THREADS] [--table TABLE] [-a [{nucleotide,protein} ...]]

Add pipeline: add sample into previous collection

options:
  -h, --help            show this help message and exit
  -g [GFF ...], --gff [GFF ...]
                        gff input files (default: None)
  -f TSV, --tsv TSV     tsv input file (default: None)
  -c COLLECTION_DIR, --collection-dir COLLECTION_DIR
                        previous collection directory (default: None)
  -s, --dont-split      dont split paralog clusters (default: False)
  -b {diamond,blast}, --blast {diamond,blast}
                        method for all-against-all alignment (default: diamond)
  -i IDENTITY, --identity IDENTITY
                        minimum percentage identity (default: 0.7)
  --LD LD               length difference cutoff between two sequences (default: 0)
  --AL AL               alignment coverage for the longer sequence (default: 0)
  --AS AS               alignment coverage for the shorter sequence (default: 0)
  -e EVALUE, --evalue EVALUE
                        Blast evalue (default: 1e-06)
  -t THREADS, --threads THREADS
                        number of threads to use, 0 for all (default: 0)
  --table TABLE         codon table (default: 11)
  -a [{nucleotide,protein} ...], --alignment [{nucleotide,protein} ...]
                        run alignment for each gene cluster (default: None)ExampleBasic:panta main -o examples/test/output -g examples/test/main/*.gff
panta add -c examples/test/output -g examples/test/add/*.gff