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).