-
--cutoff <int>, -C <int>
- filter-abund-single.py command line option
- filter-abund.py command line option
-
--keep-subsets
- do-partition.py command line option
- merge-partition.py command line option
-
--ksize <int>, -k <int>
- abundance-dist-single.py command line option
- annotate-partitions.py command line option
- count-overlap.py command line option
- do-partition.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- filter-stoptags.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- make-initial-stoptags.py command line option
- merge-partition.py command line option
- normalize-by-median.py command line option
-
--max-size <int>, -X <int>
- extract-partitions.py command line option
-
--min-partition-size <int>, -m <int>
- extract-partitions.py command line option
-
--min-tablesize <float>, -x <float>
- abundance-dist-single.py command line option
- count-overlap.py command line option
- do-partition.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- find-knots.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- make-initial-stoptags.py command line option
- normalize-by-median.py command line option
-
--n_tables <int>, -N <int>
- abundance-dist-single.py command line option
- count-overlap.py command line option
- do-partition.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- find-knots.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- make-initial-stoptags.py command line option
- normalize-by-median.py command line option
-
--no-big-traverse
- do-partition.py command line option
- partition-graph.py command line option
-
--no-build-tagset, -n
- load-graph.py command line option
-
--no-output-groups, -n
- extract-partitions.py command line option
-
--normalize-to <int>, -Z <int>
- filter-abund.py command line option
-
--output-unassigned, -U
- extract-partitions.py command line option
-
--report-total-kmers, -t
- abundance-dist-single.py command line option
- filter-abund-single.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- normalize-by-median.py command line option
-
--save-on-failure
- normalize-by-median.py command line option
-
--savetable <filename>
- abundance-dist-single.py command line option
- filter-abund-single.py command line option
-
--stoptags <filename>, -S <filename>
- make-initial-stoptags.py command line option
- partition-graph.py command line option
-
--subset-size <float>, -s <float>
- do-partition.py command line option
- make-initial-stoptags.py command line option
- partition-graph.py command line option
-
--threads <int>, -T <int>
- abundance-dist-single.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- partition-graph.py command line option
-
--threads, -T
- do-partition.py command line option
-
--variable-coverage, -V
- filter-abund.py command line option
-
--version
- abundance-dist-single.py command line option
- abundance-dist.py command line option
- annotate-partitions.py command line option
- count-median.py command line option
- count-overlap.py command line option
- do-partition.py command line option
- extract-paired-reads.py command line option
- extract-partitions.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- filter-stoptags.py command line option
- find-knots.py command line option
- interleave-reads.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- make-initial-stoptags.py command line option
- merge-partition.py command line option
- normalize-by-median.py command line option
- partition-graph.py command line option
- sample-reads-randomly.py command line option
- split-paired-reads.py command line option
-
-b, --no-bigcount
- abundance-dist-single.py command line option
- load-into-counting.py command line option
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-
-C <int>, --cutoff <int>
- normalize-by-median.py command line option
-
-d <int>, --dump-frequency <int>
- normalize-by-median.py command line option
-
-f, --fault-tolerant
- normalize-by-median.py command line option
-
-h, --help
- abundance-dist-single.py command line option
- abundance-dist.py command line option
- annotate-partitions.py command line option
- count-median.py command line option
- count-overlap.py command line option
- do-partition.py command line option
- extract-long-sequences.py command line option
- extract-paired-reads.py command line option
- extract-partitions.py command line option
- fastq-to-fasta.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- filter-stoptags.py command line option
- find-knots.py command line option
- interleave-reads.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- make-initial-stoptags.py command line option
- merge-partition.py command line option
- normalize-by-median.py command line option
- partition-graph.py command line option
- sample-reads-randomly.py command line option
- split-paired-reads.py command line option
-
-l <filename>, --loadtable <filename>
- normalize-by-median.py command line option
-
-l <int>, --length <int>
- extract-long-sequences.py command line option
-
-M <int>, --max_reads <int>
- sample-reads-randomly.py command line option
-
-N <int>, --num_reads <int>
- sample-reads-randomly.py command line option
-
-n, --n_keep
- fastq-to-fasta.py command line option
-
-o <filename>, --out <filename>
- normalize-by-median.py command line option
-
-o <filename>, --output <filename>
- interleave-reads.py command line option
-
-o <optional_output_filename>, --out <optional_output_filename>
- filter-abund.py command line option
-
-o <output_file>, --output <output_file>
- sample-reads-randomly.py command line option
-
-o, --output
- extract-long-sequences.py command line option
- fastq-to-fasta.py command line option
-
-p, --paired
- normalize-by-median.py command line option
-
-q, --quiet
- abundance-dist-single.py command line option
- count-overlap.py command line option
- do-partition.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- load-graph.py command line option
- load-into-counting.py command line option
- make-initial-stoptags.py command line option
- normalize-by-median.py command line option
-
-R <filename>, --report <filename>
- normalize-by-median.py command line option
-
-R <int>, --random-seed <int>
- sample-reads-randomly.py command line option
-
-s <filename>, --savetable <filename>
- normalize-by-median.py command line option
-
-S <int>, --samples <int>
- sample-reads-randomly.py command line option
-
-s, --squash
- abundance-dist-single.py command line option
- abundance-dist.py command line option
-
-z, --no-zero
- abundance-dist-single.py command line option
- abundance-dist.py command line option
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