usage: recursive_dbscan.py
Perform marker gene guided binning of metagenome contigs using annotations
(when available) of sequence composition, coverage and homology.
optional arguments:
-h, --help show this help message and exit
--kmers filepath Path to embedded k-mers table (default: None)
--coverages filepath Path to metagenome coverages table (default: None)
--gc-content filepath
Path to metagenome GC contents table (default: None)
--markers filepath Path to Autometa annotated markers table (default:
None)
--output-binning filepath
Path to write Autometa binning results (default: None)
--output-main filepath
Path to write Autometa main table used during/after
binning (default: None)
--clustering-method {dbscan,hdbscan}
Clustering algorithm to use for recursive binning.
(default: dbscan)
--completeness 0 < float <= 100
completeness cutoff to retain cluster. e.g. cluster
completeness >= `completeness` (default: 20.0)
--purity 0 < float <= 100
purity cutoff to retain cluster. e.g. cluster purity
>= `purity` (default: 95.0)
--cov-stddev-limit float
coverage standard deviation limit to retain cluster
e.g. cluster coverage standard deviation <= `cov-
stddev-limit` (default: 25.0)
--gc-stddev-limit float
GC content standard deviation limit to retain cluster
e.g. cluster GC content standard deviation <= `gc-
content-stddev-limit` (default: 5.0)
--taxonomy filepath Path to Autometa assigned taxonomies table (default:
None)
--starting-rank {superkingdom,phylum,class,order,family,genus,species}
Canonical rank at which to begin subsetting taxonomy
(default: superkingdom)
--reverse-ranks Reverse order at which to split taxonomy by canonical-
rank. When `--reverse-ranks` is given, contigs will be
split in order of species, genus, family, order,
class, phylum, superkingdom. (default: False)
--rank-filter {superkingdom,phylum,class,order,family,genus,species}
Taxonomy column canonical rank to subset by provided
value of `--rank-name-filter` (default: superkingdom)
--rank-name-filter RANK_NAME_FILTER
Only retrieve contigs with this name corresponding to
`--rank-filter` column (default: bacteria)
--verbose log debug information (default: False)
--cpus int Number of cores to use by clustering method (default
will try to use as many as are available) (default:
-1)