-
--bzip
- 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
- interleave-reads.py command line option
- normalize-by-median.py command line option
- sample-reads-randomly.py command line option
- split-paired-reads.py command line option
- trim-low-abund.py command line option
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--csv
- readstats.py command line option
-
--cutoff <cutoff>, -C <cutoff>
- filter-abund-single.py command line option
- filter-abund.py command line option
- trim-low-abund.py command line option
-
--diagnostics
- unique-kmers.py command line option
-
--diginorm
- trim-low-abund.py command line option
-
--diginorm-coverage <diginorm_coverage>
- trim-low-abund.py command line option
-
--error-rate <error_rate>, -e <error_rate>
- unique-kmers.py command line option
-
--force
- trim-low-abund.py command line option
-
--force_single
- normalize-by-median.py command line option
- sample-reads-randomly.py command line option
-
--fp-rate <fp_rate>
- abundance-dist-single.py command line option
- do-partition.py command line option
- filter-abund-single.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
- trim-low-abund.py command line option
-
--gzip
- 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
- interleave-reads.py command line option
- normalize-by-median.py command line option
- sample-reads-randomly.py command line option
- split-paired-reads.py command line option
- trim-low-abund.py command line option
-
--ignore-pairs
- trim-low-abund.py command line option
-
--info
- 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
- 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
- readstats.py command line option
- sample-reads-randomly.py command line option
- split-paired-reads.py command line option
- trim-low-abund.py command line option
- unique-kmers.py command line option
-
--keep-subsets
- do-partition.py command line option
- merge-partition.py command line option
-
--ksize <ksize>, -k <ksize>
- abundance-dist-single.py command line option
- annotate-partitions.py command line option
- do-partition.py command line option
- filter-abund-single.py command line option
- filter-stoptags.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
- merge-partition.py command line option
- normalize-by-median.py command line option
- trim-low-abund.py command line option
- unique-kmers.py command line option
-
--max-size <max_size>, -X <max_size>
- extract-partitions.py command line option
-
--max-tablesize <max_tablesize>, -x <max_tablesize>
- abundance-dist-single.py command line option
- do-partition.py command line option
- filter-abund-single.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
- trim-low-abund.py command line option
-
--min-partition-size <min_part_size>, -m <min_part_size>
- extract-partitions.py command line option
-
--n_tables <n_tables>, -N <n_tables>
- abundance-dist-single.py command line option
- do-partition.py command line option
- filter-abund-single.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
- trim-low-abund.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
-
--no-reformat
- interleave-reads.py command line option
-
--normalize-to <normalize_to>, -Z <normalize_to>
- filter-abund-single.py command line option
- filter-abund.py command line option
-
--output-paired <filename>, -p <filename>
- extract-paired-reads.py command line option
-
--output-single <filename>, -s <filename>
- extract-paired-reads.py command line option
-
--output-unassigned, -U
- extract-partitions.py command line option
-
--report <filename>, -R <filename>
- unique-kmers.py command line option
-
--report-frequency <report_frequency>
- normalize-by-median.py command line option
-
--savegraph <filename>
- abundance-dist-single.py command line option
- filter-abund-single.py command line option
-
--single-pass
- trim-low-abund.py command line option
-
--small-count
- abundance-dist-single.py command line option
- filter-abund-single.py command line option
- find-knots.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
- trim-low-abund.py command line option
-
--stoptags <filename>, -S <filename>
- make-initial-stoptags.py command line option
- partition-graph.py command line option
-
--stream-records, -S
- unique-kmers.py command line option
-
--subset-size <subset_size>, -s <subset_size>
- do-partition.py command line option
- make-initial-stoptags.py command line option
- partition-graph.py command line option
-
--summary-info {json,tsv}, -s {json,tsv}
- load-into-counting.py command line option
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-
--tempdir <tempdir>, -T <tempdir>
- trim-low-abund.py command line option
-
--threads <threads>, -T <threads>
- abundance-dist-single.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
- partition-graph.py command line option
-
--trim-at-coverage <trim_at_coverage>, -Z <trim_at_coverage>, --normalize-to <trim_at_coverage>
- trim-low-abund.py command line option
-
--variable-coverage, -V
- filter-abund-single.py command line option
- filter-abund.py command line option
- trim-low-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
- 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
- readstats.py command line option
- sample-reads-randomly.py command line option
- split-paired-reads.py command line option
- trim-low-abund.py command line option
- unique-kmers.py command line option
-
-0 <output_orphaned>, --output-orphaned <output_orphaned>
- split-paired-reads.py command line option
-
-1 <output_first>, --output-first <output_first>
- split-paired-reads.py command line option
-
-2 <output_second>, --output-second <output_second>
- split-paired-reads.py command line option
-
-b, --no-bigcount
- abundance-dist-single.py command line option
- abundance-dist.py command line option
- load-into-counting.py command line option
-
-C <cutoff>, --cutoff <cutoff>
- normalize-by-median.py command line option
-
-d <output_dir>, --output-dir <output_dir>
- extract-paired-reads.py command line option
-
-d <output_directory>, --output-dir <output_directory>
- split-paired-reads.py command line option
-
-f, --force
- 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
- 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
-
-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
- 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
- readstats.py command line option
- sample-reads-randomly.py command line option
- split-paired-reads.py command line option
- trim-low-abund.py command line option
- unique-kmers.py command line option
-
-l <filename>, --loadgraph <filename>
- normalize-by-median.py command line option
- trim-low-abund.py command line option
-
-l <length>, --length <length>
- extract-long-sequences.py command line option
-
-M <max_memory_usage>, --max-memory-usage <max_memory_usage>
- abundance-dist-single.py command line option
- do-partition.py command line option
- filter-abund-single.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
- trim-low-abund.py command line option
-
-M <max_reads>, --max_reads <max_reads>
- sample-reads-randomly.py command line option
-
-N <num_reads>, --num_reads <num_reads>
- sample-reads-randomly.py command line option
-
-n, --n_keep
- fastq-to-fasta.py command line option
-
-o <filename>, --output <filename>
- fastq-to-fasta.py command line option
- interleave-reads.py command line option
- normalize-by-median.py command line option
- readstats.py command line option
- sample-reads-randomly.py command line option
-
-o <optional_output_filename>, --outfile <optional_output_filename>
- filter-abund-single.py command line option
-
-o <optional_output_filename>, --output <optional_output_filename>
- filter-abund.py command line option
-
-o <output>, --output <output>
- extract-long-sequences.py command line option
-
-o <output_filename>, --output <output_filename>
- trim-low-abund.py command line option
-
-p, --paired
- normalize-by-median.py command line option
-
-q, --quiet
- abundance-dist-single.py command line option
- abundance-dist.py command line option
- filter-abund-single.py command line option
- filter-abund.py command line option
- load-into-counting.py command line option
- normalize-by-median.py command line option
- trim-low-abund.py command line option
- unique-kmers.py command line option
-
-R <random_seed>, --random-seed <random_seed>
- sample-reads-randomly.py command line option
-
-R <report_filename>, --report <report_filename>
- normalize-by-median.py command line option
-
-s <filename>, --savegraph <filename>
- normalize-by-median.py command line option
- trim-low-abund.py command line option
-
-S <num_samples>, --samples <num_samples>
- sample-reads-randomly.py command line option
-
-s, --squash
- abundance-dist-single.py command line option
- abundance-dist.py command line option
-
-U <unique_kmers>, --unique-kmers <unique_kmers>
- abundance-dist-single.py command line option
- do-partition.py command line option
- filter-abund-single.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
- trim-low-abund.py command line option
-
-u <unpaired_reads_filename>, --unpaired-reads <unpaired_reads_filename>
- normalize-by-median.py command line option
-
-z, --no-zero
- abundance-dist-single.py command line option
- abundance-dist.py command line option
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