Index

Symbols

--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 --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

--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

A

abundance-dist-single.py command line option --fp-rate <fp_rate> --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --savegraph <filename> --small-count --threads <threads>, -T <threads> --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -b, --no-bigcount -f, --force -h, --help -q, --quiet -s, --squash -z, --no-zero input_sequence_filename output_histogram_filename abundance-dist.py command line option --info --version -b, --no-bigcount -f, --force -h, --help -q, --quiet -s, --squash -z, --no-zero input_count_graph_filename input_sequence_filename output_histogram_filename

annotate-partitions.py command line option --info --ksize <ksize>, -k <ksize> --version -f, --force -h, --help graphbase input_sequence_filename

B

basename partition-graph.py command line option

C

count-median.py command line option --info --version -f, --force -h, --help input_count_graph_filename input_sequence_filename output_summary_filename

D

do-partition.py command line option --fp-rate <fp_rate> --info --keep-subsets --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --no-big-traverse --subset-size <subset_size>, -s <subset_size> --threads <threads>, -T <threads> --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -f, --force -h, --help graphbase input_sequence_filename

E

extract-long-sequences.py command line option --bzip --gzip --info --version -h, --help -l <length>, --length <length> -o <output>, --output <output> input_filenames extract-paired-reads.py command line option --bzip --gzip --info --output-paired <filename>, -p <filename> --output-single <filename>, -s <filename> --version -d <output_dir>, --output-dir <output_dir> -f, --force -h, --help infile

extract-partitions.py command line option --bzip --gzip --info --max-size <max_size>, -X <max_size> --min-partition-size <min_part_size>, -m <min_part_size> --no-output-groups, -n --output-unassigned, -U --version -f, --force -h, --help input_partition_filename output_filename_prefix

F

fastq-to-fasta.py command line option --bzip --gzip --info --version -h, --help -n, --n_keep -o <filename>, --output <filename> input_sequence filenames readstats.py command line option sample-reads-randomly.py command line option filter-abund-single.py command line option --bzip --cutoff <cutoff>, -C <cutoff> --fp-rate <fp_rate> --gzip --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --normalize-to <normalize_to>, -Z <normalize_to> --savegraph <filename> --small-count --threads <threads>, -T <threads> --variable-coverage, -V --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -f, --force -h, --help -o <optional_output_filename>, --outfile <optional_output_filename> -q, --quiet input_sequence_filename

filter-abund.py command line option --bzip --cutoff <cutoff>, -C <cutoff> --gzip --info --normalize-to <normalize_to>, -Z <normalize_to> --threads <threads>, -T <threads> --variable-coverage, -V --version -f, --force -h, --help -o <optional_output_filename>, --output <optional_output_filename> -q, --quiet input_count_graph_filename input_sequence_filename filter-stoptags.py command line option --info --ksize <ksize>, -k <ksize> --version -f, --force -h, --help input_sequence_filename input_stoptags_filename find-knots.py command line option --fp-rate <fp_rate> --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --small-count --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -f, --force -h, --help graphbase

G

graphbase annotate-partitions.py command line option do-partition.py command line option find-knots.py command line option make-initial-stoptags.py command line option merge-partition.py command line option

I

infile extract-paired-reads.py command line option split-paired-reads.py command line option input_count_graph_filename abundance-dist.py command line option count-median.py command line option filter-abund.py command line option input_filenames extract-long-sequences.py command line option trim-low-abund.py command line option input_partition_filename extract-partitions.py command line option

input_sequence fastq-to-fasta.py command line option input_sequence_filename 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 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 normalize-by-median.py command line option unique-kmers.py command line option input_stoptags_filename filter-stoptags.py command line option interleave-reads.py command line option --bzip --gzip --info --no-reformat --version -f, --force -h, --help -o <filename>, --output <filename> left right

L

left interleave-reads.py command line option load-graph.py command line option --fp-rate <fp_rate> --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --no-build-tagset, -n --threads <threads>, -T <threads> --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -f, --force -h, --help input_sequence_filename output_nodegraph_filename

load-into-counting.py command line option --fp-rate <fp_rate> --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --small-count --summary-info {json,tsv}, -s {json,tsv} --threads <threads>, -T <threads> --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -b, --no-bigcount -f, --force -h, --help -q, --quiet input_sequence_filename output_countgraph_filename

M

make-initial-stoptags.py command line option --fp-rate <fp_rate> --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --small-count --stoptags <filename>, -S <filename> --subset-size <subset_size>, -s <subset_size> --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -f, --force -h, --help graphbase

merge-partition.py command line option --info --keep-subsets --ksize <ksize>, -k <ksize> --version -f, --force -h, --help graphbase

N

normalize-by-median.py command line option --bzip --force_single --fp-rate <fp_rate> --gzip --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --report-frequency <report_frequency> --small-count --version -C <cutoff>, --cutoff <cutoff> -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -R <report_filename>, --report <report_filename> -U <unique_kmers>, --unique-kmers <unique_kmers> -f, --force -h, --help -l <filename>, --loadgraph <filename> -o <filename>, --output <filename> -p, --paired -q, --quiet -s <filename>, --savegraph <filename> -u <unpaired_reads_filename>, --unpaired-reads <unpaired_reads_filename> input_sequence_filename

O

output_countgraph_filename load-into-counting.py command line option output_filename_prefix extract-partitions.py command line option output_histogram_filename abundance-dist-single.py command line option abundance-dist.py command line option

output_nodegraph_filename load-graph.py command line option output_summary_filename count-median.py command line option

P

partition-graph.py command line option --info --no-big-traverse --stoptags <filename>, -S <filename> --subset-size <subset_size>, -s <subset_size> --threads <threads>, -T <threads> --version -f, --force -h, --help basename

R

readstats.py command line option --csv --info --version -h, --help -o <filename>, --output <filename> filenames

right interleave-reads.py command line option

S

sample-reads-randomly.py command line option --bzip --force_single --gzip --info --version -M <max_reads>, --max_reads <max_reads> -N <num_reads>, --num_reads <num_reads> -R <random_seed>, --random-seed <random_seed> -S <num_samples>, --samples <num_samples> -f, --force -h, --help -o <filename>, --output <filename> filenames

split-paired-reads.py command line option --bzip --gzip --info --version -0 <output_orphaned>, --output-orphaned <output_orphaned> -1 <output_first>, --output-first <output_first> -2 <output_second>, --output-second <output_second> -d <output_directory>, --output-dir <output_directory> -f, --force -h, --help infile

T

trim-low-abund.py command line option --bzip --cutoff <cutoff>, -C <cutoff> --diginorm --diginorm-coverage <diginorm_coverage> --force --fp-rate <fp_rate> --gzip --ignore-pairs --info --ksize <ksize>, -k <ksize> --max-tablesize <max_tablesize>, -x <max_tablesize> --n_tables <n_tables>, -N <n_tables> --single-pass --small-count --tempdir <tempdir>, -T <tempdir> --trim-at-coverage <trim_at_coverage>, -Z <trim_at_coverage>, --normalize-to <trim_at_coverage> --variable-coverage, -V --version -M <max_memory_usage>, --max-memory-usage <max_memory_usage> -U <unique_kmers>, --unique-kmers <unique_kmers> -h, --help -l <filename>, --loadgraph <filename> -o <output_filename>, --output <output_filename> -q, --quiet -s <filename>, --savegraph <filename> input_filenames

U

unique-kmers.py command line option --diagnostics --error-rate <error_rate>, -e <error_rate> --info --ksize <ksize>, -k <ksize> --report <filename>, -R <filename> --stream-records, -S --version -h, --help -q, --quiet input_sequence_filename