---
name: "average_nucleotide_identity.py"
section: "1"
platform: "linux"
package: "python3-pyani"
version: "0.2.13-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/average_nucleotide_identity.py"
---

# average\_nucleotide\_identity.py(1)

average nucleotide identity

## 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.