AVERAGE_NUCLEOTIDE_IDENTITY.PY(1)

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.