Index

Symbols

--attribute=<KEY>:<REGULAR_PATTERN> command line option, [1], [2] --cache-size=INTEGER command line option --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> command line option --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> command line option, [1], [2] --index-file=<FILENAME> command line option --length command line option --local=<DIRNAME> command line option, [1] --median command line option --merge-ids command line option --merge=<KEY> command line option --minimum-circle=FLOAT command line option --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> command line option --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> command line option --require-rank=<RANK_NAME> taxonomy command line option, [1], [2], [3] --run=<PYTHON_EXPRESSION> command line option --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> command line option --seq-rank command line option --set-identifier=<PYTHON_EXPRESSION> command line option --set-sequence=<PYTHON_EXPRESSION> command line option --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> command line option --tag-list=<FILENAME> command line option --uniq-id command line option --uppercase obitools command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --with-taxon-at-rank=<RANK_NAME> command line option -3 <INTEGER> command line option -A command line option -a command line option -A <ANCESTOR>, --restricting_ancestor=<ANCESTOR> command line option -a <ANCESTOR>, --restricting_ancestor=<ANCESTOR> command line option -A <ATTRIBUTE_NAME>, --has-attribute=<KEY> command line option, [1], [2] -a <FLOAT> command line option, [1] -a <IUPAC_PATTERN>, --accepted=<IUPAC_PATTERN> command line option -a <KEY>, --mean=<KEY> command line option -a <KEY>, --omit-attribute=<KEY> command line option -a <KEY>:<REGULAR_PATTERN>, command line option, [1], [2] -a <TAXON_INFOS>, --add-taxon=<TAXON_INFOS> command line option -a, --all command line option -a, --approx-sampling command line option -a, --mean command line option -b <INTEGER>, --begin=<INTEGER> command line option -c command line option, [1] -c <KEY>, --category-attribute=<KEY> command line option, [1], [2] -C, --clear command line option -C, --cluster command line option -D command line option -d ###, --distance=### command line option -d <filename> command line option, [1], [2] -d <FILENAME>, --database=<FILENAME> taxonomy command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] -D <INTEGER> command line option -d <INTEGER>, --distance=<INTEGER> command line option -D <REGULAR_PATTERN>, --definition=<REGULAR_PATTERN> command line option, [1], [2] -D <TAXID>, --delete-local-taxon=<TAXID> command line option -d, --no-definition command line option -E <FILENAME>, --extract-list=<FILENAME> command line option -e <INTEGER> command line option, [1] -e <INTEGER>, --end=<INTEGER> command line option -e <SAMPLE_NAME>, --extract=<KEY> command line option -E <TAXID> command line option -E FLOAT, --errors=FLOAT command line option -e INT, --errors=<INT> command line option -e, --error command line option -f command line option -f ###, --family-size=### command line option -F <FILE_NAME>, --file-name=<FILE_NAME> command line option -f <FORMAT>, --format=<FORMAT> command line option -f <TAXON_NAME>:<TAXID>, --add-favorite-name=<TAXON_NAME>:<TAXID> command line option -f FUNCTION, --function=FUNCTION command line option -g ###, --gc-max=### command line option -g <FILENAME>, --genus_found=<FILENAME> command line option -g, --graph command line option -h command line option, [1], [2] -H, --head command line option -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 command line option -I <REGULAR_PATTERN>, --identifier=<REGULAR_PATTERN> command line option, [1], [2]

-i <TAXID> command line option, [1] -i <TAXID>, --ignore=<TAXID> taxonomy command line option, [1], [2], [3] -k command line option -k <KEY>, --keep=<KEY> command line option -k <KEY>, --key-name=<KEY> command line option -k <KEY>, --key=<KEY> command line option -k <KEY_NAME>, --key-name=<KEY_NAME> command line option -L command line option -L <##>, --lmax=<##> command line option, [1], [2] -l <##>, --lmin=<##> command line option, [1], [2] -l <FILENAME>, --sample-list=<FILENAME>, command line option -L <filename>, --oligo-list=<filename> command line option -L <INTEGER> command line option, [1] -l <INTEGER> command line option, [1] -l, --lsu command line option -m <####>, --min-taxid=<####> command line option -m <1|2> command line option, [1] -M <KEY>, --max=<KEY> command line option -m <KEY>, --merge=<KEY> command line option -m <KEY>, --min=<KEY> command line option -m <MCLFILE>, --mcl=<MCLFILE> command line option -m FLOAT, --minimum-identity=FLOAT command line option -M, --max command line option -m, --min command line option -n , --nr command line option -n <INT>, --number=<INT> command line option -n <INTEGER>, --number=<INTEGER> command line option -n <INTEGER>, --sequence-count <INTEGER> command line option -n <INTEGER>, --sequence-count=<INTEGER> command line option -n <NOT AVAILABLE STRING>, --na-string=<NOT AVAILABLE STRING> command line option -n <SAMPLEIDS>, --sample-name=<SAMPLEIDS>, command line option -O <INTEGER> command line option -o <TAGNAME>, --other-tag=<TAGNAME>, command line option -O, --only-valid-python command line option -o, --output-seq command line option -P command line option -p command line option -P ###, --homopolymer-min=### command line option -p ###, --homopolymer=### command line option -p , --parc command line option -p <PATH>, --path=<PATH> command line option -p <PREFIX FILENAME>, --prefix=<PREFIX FILENAME> command line option -p <PYTHON_EXPRESSION>, --predicat=<PYTHON_EXPRESSION> command line option, [1], [2] -p <REGEX>, --sample-pattern=<REGEX>, command line option -p <STRING>, --prefix=<STRING> command line option -p, --prefix command line option -q <FLOAT> command line option -r command line option -r , --ref command line option -R <FILENAME>, --ref-database=<FILENAME> command line option -r <FILENAME>, --reverse-reads=<FILENAME> command line option, [1] -r <FLOAT>, --ratio=<FLOAT> command line option -r <IUPAC_PATTERN>, --rejected=<IUPAC_PATTERN> command line option -R <OLD_NAME>:<NEW_NAME>, --rename-tag=<OLD_NAME>:<NEW_NAME> command line option -r <TAXID> command line option, [1] -r <TAXID>, --required=<TAXID> taxonomy command line option, [1], [2], [3] -R <TEXT> command line option -r TAXID, --required=<TAXID> command line option -r, --reverse command line option, [1] -S command line option -s command line option -s ###, --oligo-size=### command line option -s ###, --sample-size ### command line option -s , --ssu command line option -s <FLOAT> command line option -s <KEY>, --sample=<KEY> command line option, [1] -s <KEY>, -std-dev=<KEY> command line option -S <KEY>:<PYTHON_EXPRESSION>, --set-tag=<KEY>:<PYTHON_EXPRESSION> command line option -s <REGULAR_PATTERN>, --sequence=<REGULAR_PATTERN> command line option, [1], [2] -s <SPECIES_NAME>, --add-species=<SPECIES_NAME> command line option -s <TAGNAME>, --sample=<TAGNAME>, command line option -s, --sequence command line option -t , --trunc command line option -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> command line option -T <seconde>, --timeout=<seconde> command line option -t <TAXONOMIC_LEVEL> command line option -T, --set-definition=<PYTHON_EXPRESSION> command line option -t, --tag-list command line option -U command line option -u <FILENAME>, --undefined=<FILENAME> command line option -u <FILENAME>, --unidentified=<FILENAME> command line option -u, --unidentified command line option -u, --uniq command line option -v command line option -v <KEY>, --variance=<KEY> command line option -v, --inverse-match command line option, [1], [2] -w, --without-replacement command line option -x <FLOAT> command line option -x RANK, --explain=RANK command line option

C

command line option --attribute=<KEY>:<REGULAR_PATTERN>, [1], [2] --cache-size=INTEGER --delete-tag=<KEY> --id-list=<FILENAME>, [1], [2] --index-file=<FILENAME> --length --local=<DIRNAME>, [1] --median --merge-ids --merge=<KEY> --minimum-circle=FLOAT --output-field-separator=<STRING> --rank=<TAXONOMIC_RANK> --run=<PYTHON_EXPRESSION> --score-min=<FLOAT> --seq-rank --set-identifier=<PYTHON_EXPRESSION> --set-sequence=<PYTHON_EXPRESSION> --sort=<KEY> --tag-list=<FILENAME> --uniq-id --with-taxon-at-rank=<RANK_NAME> -3 <INTEGER> -A -A <ANCESTOR>, --restricting_ancestor=<ANCESTOR> -A <ATTRIBUTE_NAME>, --has-attribute=<KEY>, [1], [2] -C, --clear -C, --cluster -D -D <INTEGER> -D <REGULAR_PATTERN>, --definition=<REGULAR_PATTERN>, [1], [2] -D <TAXID>, --delete-local-taxon=<TAXID> -E <FILENAME>, --extract-list=<FILENAME> -E <TAXID> -E FLOAT, --errors=FLOAT -F <FILE_NAME>, --file-name=<FILE_NAME> -H, --head -I <REGULAR_PATTERN>, --identifier=<REGULAR_PATTERN>, [1], [2] -L -L <##>, --lmax=<##>, [1], [2] -L <INTEGER>, [1] -L <filename>, --oligo-list=<filename> -M <KEY>, --max=<KEY> -M, --max -O <INTEGER> -O, --only-valid-python -P -P ###, --homopolymer-min=### -R <FILENAME>, --ref-database=<FILENAME> -R <OLD_NAME>:<NEW_NAME>, --rename-tag=<OLD_NAME>:<NEW_NAME> -R <TEXT> -S -S <KEY>:<PYTHON_EXPRESSION>, --set-tag=<KEY>:<PYTHON_EXPRESSION> -T <seconde>, --timeout=<seconde> -T, --set-definition=<PYTHON_EXPRESSION> -U -a -a <ANCESTOR>, --restricting_ancestor=<ANCESTOR> -a <FLOAT>, [1] -a <IUPAC_PATTERN>, --accepted=<IUPAC_PATTERN> -a <KEY>, --mean=<KEY> -a <KEY>, --omit-attribute=<KEY> -a <KEY>:<REGULAR_PATTERN>,, [1], [2] -a <TAXON_INFOS>, --add-taxon=<TAXON_INFOS> -a, --all -a, --approx-sampling -a, --mean -b <INTEGER>, --begin=<INTEGER> -c, [1] -c <KEY>, --category-attribute=<KEY>, [1], [2] -d ###, --distance=### -d <INTEGER>, --distance=<INTEGER> -d <filename>, [1], [2] -d, --no-definition -e <INTEGER>, [1] -e <INTEGER>, --end=<INTEGER> -e <SAMPLE_NAME>, --extract=<KEY> -e INT, --errors=<INT> -e, --error -f -f ###, --family-size=### -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, [1], [2] -i , --merge-ids -i <TAXID>, [1] -k -k <KEY>, --keep=<KEY> -k <KEY>, --key-name=<KEY> -k <KEY>, --key=<KEY> -k <KEY_NAME>, --key-name=<KEY_NAME> -l <##>, --lmin=<##>, [1], [2] -l <FILENAME>, --sample-list=<FILENAME>, -l <INTEGER>, [1] -l, --lsu -m <####>, --min-taxid=<####> -m <1|2>, [1] -m <KEY>, --merge=<KEY> -m <KEY>, --min=<KEY> -m <MCLFILE>, --mcl=<MCLFILE> -m FLOAT, --minimum-identity=FLOAT -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 <TAGNAME>, --other-tag=<TAGNAME>, -o, --output-seq -p -p ###, --homopolymer=### -p , --parc -p <PATH>, --path=<PATH> -p <PREFIX FILENAME>, --prefix=<PREFIX FILENAME> -p <PYTHON_EXPRESSION>, --predicat=<PYTHON_EXPRESSION>, [1], [2] -p <REGEX>, --sample-pattern=<REGEX>, -p <STRING>, --prefix=<STRING> -p, --prefix -q <FLOAT> -r -r , --ref -r <FILENAME>, --reverse-reads=<FILENAME>, [1] -r <FLOAT>, --ratio=<FLOAT> -r <IUPAC_PATTERN>, --rejected=<IUPAC_PATTERN> -r <TAXID>, [1] -r TAXID, --required=<TAXID> -r, --reverse, [1] -s -s ###, --oligo-size=### -s ###, --sample-size ### -s , --ssu -s <FLOAT> -s <KEY>, --sample=<KEY>, [1] -s <KEY>, -std-dev=<KEY> -s <REGULAR_PATTERN>, --sequence=<REGULAR_PATTERN>, [1], [2] -s <SPECIES_NAME>, --add-species=<SPECIES_NAME> -s <TAGNAME>, --sample=<TAGNAME>, -s, --sequence -t , --trunc -t <KEY>, --tag-name=<KEY> -t <TAXONOMIC_LEVEL> -t, --tag-list -u <FILENAME>, --undefined=<FILENAME> -u <FILENAME>, --unidentified=<FILENAME> -u, --unidentified -u, --uniq -v -v <KEY>, --variance=<KEY> -v, --inverse-match, [1], [2] -w, --without-replacement -x <FLOAT> -x RANK, --explain=RANK Filename points to the file containing the illumina index reads

E

ecodbtaxstat (module) ecotag (module)

ecotaxspecificity (module) ecotaxstat (module)

F

Filename points to the file containing the illumina index reads command line option

I

illuminapairedend (module)

N

ngsfilter (module)

O

obiaddtaxids (module) obiannotate (module) obiclean (module) obicomplement (module) obiconvert (module) obicount (module) obicut (module) obidistribute (module) obiextract (module) obigrep (module) obihead (module) obijoinpairedend (module) obipr2 (module)

obisample (module) obiselect (module) obisilva (module) obisort (module) obisplit (module) obistat (module) obisubset (module) obitab (module) obitail (module) obitaxonomy (module) obitools command line option --DEBUG, [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] --ecopcr, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --ecopcrdb, [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>, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --embl, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --fasta, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --fasta-output, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --fastq-output, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --genbank, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --nuc, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --only <N>, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --prot, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --sanger, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] --skip <N>, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21] --solexa, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22] --uppercase, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] -h, --help, [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] obiuniq (module) oligotag (module)

T

taxonomy command line option --require-rank=<RANK_NAME>, [1], [2], [3] -d <FILENAME>, --database=<FILENAME>, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12] -i <TAXID>, --ignore=<TAXID>, [1], [2], [3] -r <TAXID>, --required=<TAXID>, [1], [2], [3] -t <FILENAME>, --taxonomy-dump=<FILENAME>, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]