Index

Symbols | A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | U

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 <int>, -C <int>
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
--error-rate <float>, -e <float>
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 <float>
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
--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
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 <int>, -X <int>
extract-partitions.py command line option
--max-tablesize <float>, -x <float>
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 <int>, -m <int>
extract-partitions.py command line option
--n_tables <int>, -N <int>
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
--normalize-to <int>, -Z <int>
filter-abund.py command line option
trim-low-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
--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 <float>, -s <float>
do-partition.py command line option
make-initial-stoptags.py command line option
partition-graph.py command line option
--summary-info <format>, -s <format>
load-into-counting.py command line option
--tempdir <str>, -T <str>
trim-low-abund.py command line option
--threads <int>, -T <int>
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
--variable-coverage, -V
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 <int>, --cutoff <int>
normalize-by-median.py command line option
-d <output_directory>, --output-dir <output_directory>
split-paired-reads.py command line option
-d, --output-dir
extract-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 <int>, --length <int>
extract-long-sequences.py command line option
-M <float>, --max-memory-usage <float>
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 <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>, --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>, --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
normalize-by-median.py command line option
unique-kmers.py command line option
-R <int>, --random-seed <int>
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 <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
-U <float>, --unique-kmers <float>
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 <float>
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--savegraph <filename>
--threads <int>, -T <int>
--version
-M <float>, --max-memory-usage <float>
-U <float>, --unique-kmers <float>
-b, --no-bigcount
-f, --force
-h, --help
-s, --squash
-z, --no-zero
input_sequence_filename
output_histogram_filename
abundance-dist.py command line option
--version
-b, --no-bigcount
-f, --force
-h, --help
-s, --squash
-z, --no-zero
input_count_graph_filename
input_sequence_filename
output_histogram_filename
annotate-partitions.py command line option
--ksize <int>, -k <int>
--version
-f, --force
-h, --help
graphbase
input_sequence_filename

B

basename
partition-graph.py command line option

C

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

D

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

E

extract-long-sequences.py command line option
--bzip
--gzip
--version
-h, --help
-l <int>, --length <int>
-o <output>, --output <output>
input_filenames
extract-paired-reads.py command line option
--bzip
--gzip
--output-paired <filename>, -p <filename>
--output-single <filename>, -s <filename>
--version
-d, --output-dir
-f, --force
-h, --help
infile
extract-partitions.py command line option
--bzip
--gzip
--max-size <int>, -X <int>
--min-partition-size <int>, -m <int>
--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
--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 <int>, -C <int>
--fp-rate <float>
--gzip
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--savegraph <filename>
--threads <int>, -T <int>
--version
-M <float>, --max-memory-usage <float>
-U <float>, --unique-kmers <float>
-f, --force
-h, --help
input_sequence_filename
filter-abund.py command line option
--bzip
--cutoff <int>, -C <int>
--gzip
--normalize-to <int>, -Z <int>
--threads <int>, -T <int>
--variable-coverage, -V
--version
-f, --force
-h, --help
-o <optional_output_filename>, --output <optional_output_filename>
input_count_graph_filename
input_sequence_filename
filter-stoptags.py command line option
--ksize <int>, -k <int>
--version
-f, --force
-h, --help
input_sequence_filename
input_stoptags_filename
find-knots.py command line option
--fp-rate <float>
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--version
-M <float>, --max-memory-usage <float>
-U <float>, --unique-kmers <float>
-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
--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 <float>
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--no-build-tagset, -n
--threads <int>, -T <int>
--version
-M <float>, --max-memory-usage <float>
-U <float>, --unique-kmers <float>
-f, --force
-h, --help
input_sequence_filename
output_nodegraph_filename
load-into-counting.py command line option
--fp-rate <float>
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--summary-info <format>, -s <format>
--threads <int>, -T <int>
--version
-M <float>, --max-memory-usage <float>
-U <float>, --unique-kmers <float>
-b, --no-bigcount
-f, --force
-h, --help
input_sequence_filename
output_countgraph_filename

M

make-initial-stoptags.py command line option
--fp-rate <float>
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--stoptags <filename>, -S <filename>
--subset-size <float>, -s <float>
--version
-M <float>, --max-memory-usage <float>
-U <float>, --unique-kmers <float>
-f, --force
-h, --help
graphbase
merge-partition.py command line option
--keep-subsets
--ksize <int>, -k <int>
--version
-f, --force
-h, --help
graphbase

N

normalize-by-median.py command line option
--bzip
--force_single
--fp-rate <float>
--gzip
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--report-frequency <report_frequency>
--version
-C <int>, --cutoff <int>
-M <float>, --max-memory-usage <float>
-R <report_filename>, --report <report_filename>
-U <float>, --unique-kmers <float>
-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
--no-big-traverse
--stoptags <filename>, -S <filename>
--subset-size <float>, -s <float>
--threads <int>, -T <int>
--version
-f, --force
-h, --help
basename

R

readstats.py command line option
--csv
--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
--version
-M <int>, --max_reads <int>
-N <int>, --num_reads <int>
-R <int>, --random-seed <int>
-S <int>, --samples <int>
-f, --force
-h, --help
-o <filename>, --output <filename>
filenames
split-paired-reads.py command line option
--bzip
--gzip
--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 <int>, -C <int>
--force
--fp-rate <float>
--gzip
--ignore-pairs
--ksize <int>, -k <int>
--max-tablesize <float>, -x <float>
--n_tables <int>, -N <int>
--normalize-to <int>, -Z <int>
--tempdir <str>, -T <str>
--variable-coverage, -V
--version
-M <float>, --max-memory-usage <float>
-U <float>, --unique-kmers <float>
-h, --help
-l <filename>, --loadgraph <filename>
-o <output_filename>, --output <output_filename>
-s <filename>, --savegraph <filename>
input_filenames

U

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