-
--attribute=<KEY>:<REGULAR_PATTERN>
-
--cache-size=INTEGER
-
--DEBUG
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29]
-
--delete-tag=<KEY>
-
--ecopcr
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--ecopcrdb
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--ecopcrdb-output=<PREFIX_FILENAME>
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]
-
--embl
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--fasta
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--fasta-output
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]
-
--fastq-output
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]
-
--genbank
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--id-list=<FILENAME>
-
--index-file=<FILENAME>
-
--length
-
--local=<DIRNAME>
-
--median
-
--merge-ids
-
--merge=<KEY>
-
--minimum-circle=FLOAT
-
--nuc
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--only <N>
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--output-field-separator=<STRING>
-
--prot
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--rank=<TAXONOMIC_RANK>
-
--require-rank=<RANK_NAME>
-
--run=<PYTHON_EXPRESSION>
-
--sanger
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22]
-
--score-min=<FLOAT>
-
--seq-rank
-
--set-identifier=<PYTHON_EXPRESSION>
-
--set-sequence=<PYTHON_EXPRESSION>
-
--skip <N>
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21]
-
--solexa
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22]
-
--sort=<KEY>
-
--tag-list=<FILENAME>
-
--uniq-id
-
--uppercase
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]
-
--with-taxon-at-rank=<RANK_NAME>
-
-3 <INTEGER>
-
-A
-
-a
-
-A <ANCESTOR>, --restricting_ancestor=<ANCESTOR>
-
-a <ANCESTOR>, --restricting_ancestor=<ANCESTOR>
-
-A <ATTRIBUTE_NAME>, --has-attribute=<KEY>
-
-a <FLOAT>
-
-a <IUPAC_PATTERN>, --accepted=<IUPAC_PATTERN>
-
-a <KEY>, --mean=<KEY>
-
-a <KEY>, --omit-attribute=<KEY>
-
-a <KEY>:<REGULAR_PATTERN>,
-
-a <TAXON_INFOS>, --add-taxon=<TAXON_INFOS>
-
-a, --all
-
-a, --approx-sampling
-
-a, --mean
-
-b <INTEGER>, --begin=<INTEGER>
-
-c
-
-c <KEY>, --category-attribute=<KEY>
-
-C, --clear
-
-C, --cluster
-
-D
-
-d ###, --distance=###
-
-d <filename>
-
-d <FILENAME>, --database=<FILENAME>
- taxonomy command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]
-
-D <INTEGER>
-
-d <INTEGER>, --distance=<INTEGER>
-
-D <REGULAR_PATTERN>, --definition=<REGULAR_PATTERN>
-
-D <TAXID>, --delete-local-taxon=<TAXID>
-
-d, --no-definition
-
-E <FILENAME>, --extract-list=<FILENAME>
-
-e <INTEGER>
-
-e <INTEGER>, --end=<INTEGER>
-
-e <SAMPLE_NAME>, --extract=<KEY>
-
-E <TAXID>
-
-E FLOAT, --errors=FLOAT
-
-e INT, --errors=<INT>
-
-e, --error
-
-f
-
-f ###, --family-size=###
-
-F <FILE_NAME>, --file-name=<FILE_NAME>
-
-f <FORMAT>, --format=<FORMAT>
-
-f <TAXON_NAME>:<TAXID>, --add-favorite-name=<TAXON_NAME>:<TAXID>
-
-f FUNCTION, --function=FUNCTION
-
-g ###, --gc-max=###
-
-g <FILENAME>, --genus_found=<FILENAME>
-
-g, --graph
-
-h
-
-H, --head
-
-h, --help
- obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29]
-
-i , --merge-ids
-
-I <REGULAR_PATTERN>, --identifier=<REGULAR_PATTERN>
-
-i <TAXID>
|
-
-i <TAXID>, --ignore=<TAXID>
-
-k
-
-k <KEY>, --keep=<KEY>
-
-k <KEY>, --key-name=<KEY>
-
-k <KEY>, --key=<KEY>
-
-k <KEY_NAME>, --key-name=<KEY_NAME>
-
-L
-
-L <##>, --lmax=<##>
-
-l <##>, --lmin=<##>
-
-l <FILENAME>, --sample-list=<FILENAME>,
-
-L <filename>, --oligo-list=<filename>
-
-L <INTEGER>
-
-l <INTEGER>
-
-l, --lsu
-
-m <####>, --min-taxid=<####>
-
-m <1|2>
-
-M <KEY>, --max=<KEY>
-
-m <KEY>, --merge=<KEY>
-
-m <KEY>, --min=<KEY>
-
-m <MCLFILE>, --mcl=<MCLFILE>
-
-m FLOAT, --minimum-identity=FLOAT
-
-M INTEGER, --min-matches=FLOAT
-
-M, --max
-
-m, --min
-
-n , --nr
-
-n <INT>, --number=<INT>
-
-n <INTEGER>, --number=<INTEGER>
-
-n <INTEGER>, --sequence-count <INTEGER>
-
-n <INTEGER>, --sequence-count=<INTEGER>
-
-n <NOT AVAILABLE STRING>, --na-string=<NOT AVAILABLE STRING>
-
-n <SAMPLEIDS>, --sample-name=<SAMPLEIDS>,
-
-O <INTEGER>
-
-o <TAGNAME>, --other-tag=<TAGNAME>,
-
-O, --only-valid-python
-
-o, --output-seq
-
-P
-
-p
-
-P ###, --homopolymer-min=###
-
-p ###, --homopolymer=###
-
-p , --parc
-
-p <PATH>, --path=<PATH>
-
-p <PREFIX FILENAME>, --prefix=<PREFIX FILENAME>
-
-p <PYTHON_EXPRESSION>, --predicat=<PYTHON_EXPRESSION>
-
-p <REGEX>, --sample-pattern=<REGEX>,
-
-p <STRING>, --prefix=<STRING>
-
-p, --prefix
-
-q <FLOAT>
-
-r
-
-r , --ref
-
-R <FILENAME>, --ref-database=<FILENAME>
-
-r <FILENAME>, --reverse-reads=<FILENAME>
-
-r <FLOAT>, --ratio=<FLOAT>
-
-r <IUPAC_PATTERN>, --rejected=<IUPAC_PATTERN>
-
-R <OLD_NAME>:<NEW_NAME>, --rename-tag=<OLD_NAME>:<NEW_NAME>
-
-r <TAXID>
-
-r <TAXID>, --required=<TAXID>
-
-R <TEXT>
-
-r TAXID, --required=<TAXID>
-
-r, --reverse
-
-S
-
-s
-
-s ###, --oligo-size=###
-
-s ###, --sample-size ###
-
-s , --ssu
-
-s <FLOAT>
-
-s <KEY>, --sample=<KEY>
-
-s <KEY>, -std-dev=<KEY>
-
-S <KEY>:<PYTHON_EXPRESSION>, --set-tag=<KEY>:<PYTHON_EXPRESSION>
-
-s <REGULAR_PATTERN>, --sequence=<REGULAR_PATTERN>
-
-s <SPECIES_NAME>, --add-species=<SPECIES_NAME>
-
-s <TAGNAME>, --sample=<TAGNAME>,
-
-s, --sequence
-
-t , --trunc
-
-t <FILENAME>, --taxonomy-dump=<FILENAME>
- taxonomy command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]
-
-t <KEY>, --tag-name=<KEY>
-
-T <seconde>, --timeout=<seconde>
-
-t <TAXONOMIC_LEVEL>
-
-T, --set-definition=<PYTHON_EXPRESSION>
-
-t, --tag-list
-
-U
-
-u <FILENAME>, --undefined=<FILENAME>
-
-u <FILENAME>, --unidentified=<FILENAME>
-
-u, --unidentified
-
-u, --uniq
-
-v
-
-v <KEY>, --variance=<KEY>
-
-v, --inverse-match
-
-w, --without-replacement
-
-x <FLOAT>
-
-x RANK, --explain=RANK
|