NAME

       average_nucleotide_identity.py - average nucleotide identity

DESCRIPTION

       usage: average_nucleotide_identity.py [-h] [--version] -o OUTDIRNAME -i

       INDIRNAME [-v] [-f] [-s FRAGSIZE]
              [-l LOGFILE] [--skip_nucmer] [--skip_blastn] [--noclobber] [--nocompress] [-g] [--gformat GFORMAT]
              [--gmethod {mpl,seaborn}] [--labels LABELS] [--classes CLASSES] [-m {ANIm,ANIb,ANIblastall,TETRA}]
              [--scheduler  {multiprocessing,SGE}]  [--workers WORKERS] [--SGEgroupsize SGEGROUPSIZE] [--SGEargs
              SGEARGS]  [--maxmatch]   [--nucmer_exe   NUCMER_EXE]   [--filter_exe   FILTER_EXE]   [--blastn_exe
              BLASTN_EXE]  [--makeblastdb_exe  MAKEBLASTDB_EXE]  [--blastall_exe  BLASTALL_EXE]  [--formatdb_exe
              FORMATDB_EXE] [--write_excel] [--rerender]  [--subsample  SUBSAMPLE]  [--seed  SEED]  [--jobprefix
              JOBPREFIX]

   optional arguments:
       -h, --help
              show this help message and exit

       --version
              show program's version number and exit

       -o OUTDIRNAME, --outdir OUTDIRNAME
              Output directory (required)

       -i INDIRNAME, --indir INDIRNAME
              Input directory name (required)

       -v, --verbose
              Give verbose output

       -f, --force
              Force file overwriting

       -s FRAGSIZE, --fragsize FRAGSIZE
              Sequence fragment size for ANIb (default 1020)

       -l LOGFILE, --logfile LOGFILE
              Logfile location

       --skip_nucmer
              Skip NUCmer runs, for testing (e.g. if output already present)

       --skip_blastn
              Skip BLASTN runs, for testing (e.g. if output already present)

       --noclobber
              Don't nuke existing files

       --nocompress
              Don't compress/delete the comparison output

       -g, --graphics
              Generate heatmap of ANI

       --gformat GFORMAT
              Graphics output format(s) [pdf|png|jpg|svg] (default pdf,png,eps meaning three file formats)

       --gmethod {mpl,seaborn}
              Graphics output method (default mpl)

       --labels LABELS
              Path to file containing sequence labels

       --classes CLASSES
              Path to file containing sequence classes

       -m {ANIm,ANIb,ANIblastall,TETRA}, --method {ANIm,ANIb,ANIblastall,TETRA}
              ANI method (default ANIm)

       --scheduler {multiprocessing,SGE}
              Job scheduler (default multiprocessing, i.e. locally)

       --workers WORKERS
              Number of worker processes for multiprocessing (default zero, meaning use all available cores)

       --SGEgroupsize SGEGROUPSIZE
              Number of jobs to place in an SGE array group (default 10000)

       --SGEargs SGEARGS
              Additional arguments for qsub

       --maxmatch
              Override MUMmer to allow all NUCmer matches

       --nucmer_exe NUCMER_EXE
              Path to NUCmer executable

       --filter_exe FILTER_EXE
              Path to delta-filter executable

       --blastn_exe BLASTN_EXE
              Path to BLASTN+ executable

       --makeblastdb_exe MAKEBLASTDB_EXE
              Path to BLAST+ makeblastdb executable

       --blastall_exe BLASTALL_EXE
              Path to BLASTALL executable

       --formatdb_exe FORMATDB_EXE
              Path to BLAST formatdb executable

       --write_excel
              Write Excel format output tables

       --rerender
              Rerender graphics output without recalculation

       --subsample SUBSAMPLE
              Subsample a percentage [0-1] or specific number (1-n) of input sequences

       --seed SEED
              Set random seed for reproducible subsampling.

       --jobprefix JOBPREFIX
              Prefix for SGE jobs (default ANI).

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

average_nucleotide_identity.py 0.2.11               July 2021                  AVERAGE_NUCLEOTIDE_IDENTITY.PY(1)