Navigation
index
khmer 3.0.0~a3+dfsg-7 documentation
»
Index
Docs
Index
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
filter-abund-single.py command line option
filter-abund.py command line option
normalize-by-median.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
trim-low-abund.py command line option
--error-rate
unique-kmers.py command line option
--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
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
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
--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
--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
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
--length
extract-long-sequences.py command line option
--loadgraph
normalize-by-median.py command line option
trim-low-abund.py command line option
--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
--max-size
extract-partitions.py command line option
--max_reads
sample-reads-randomly.py command line option
--min-partition-size
extract-partitions.py command line option
--n_keep
fastq-to-fasta.py command line option
--no-big-traverse
do-partition.py command line option
partition-graph.py command line option
--no-bigcount
abundance-dist-single.py command line option
abundance-dist.py command line option
load-into-counting.py command line option
--no-build-tagset
load-graph.py command line option
--no-output-groups
extract-partitions.py command line option
--no-reformat
interleave-reads.py command line option
--no-zero
abundance-dist-single.py command line option
abundance-dist.py command line option
--normalize-to
filter-abund-single.py command line option
filter-abund.py command line option
trim-low-abund.py command line option
--num_reads
sample-reads-randomly.py command line option
--outfile
filter-abund-single.py command line option
--output
extract-long-sequences.py command line option
fastq-to-fasta.py command line option
filter-abund.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
trim-low-abund.py command line option
--output-dir
extract-paired-reads.py command line option
split-paired-reads.py command line option
--output-first
split-paired-reads.py command line option
--output-orphaned
split-paired-reads.py command line option
--output-paired
extract-paired-reads.py command line option
--output-second
split-paired-reads.py command line option
--output-single
extract-paired-reads.py command line option
--output-unassigned
extract-partitions.py command line option
--paired
normalize-by-median.py command line option
--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
--random-seed
sample-reads-randomly.py command line option
--report
normalize-by-median.py command line option
unique-kmers.py command line option
--report-frequency
normalize-by-median.py command line option
--samples
sample-reads-randomly.py command line option
--savegraph
abundance-dist-single.py command line option
filter-abund-single.py command line option
normalize-by-median.py command line option
trim-low-abund.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
--squash
abundance-dist-single.py command line option
abundance-dist.py command line option
--stoptags
make-initial-stoptags.py command line option
partition-graph.py command line option
--stream-records
unique-kmers.py command line option
--subset-size
do-partition.py command line option
make-initial-stoptags.py command line option
partition-graph.py command line option
--summary-info
load-into-counting.py command line option
trim-low-abund.py command line option
--tempdir
trim-low-abund.py command line option
--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-low-abund.py command line option
--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
--unpaired-reads
normalize-by-median.py command line option
--variable-coverage
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
split-paired-reads.py command line option
-1
split-paired-reads.py command line option
-2
split-paired-reads.py command line option
-b
abundance-dist-single.py command line option
abundance-dist.py command line option
load-into-counting.py command line option
-C
filter-abund-single.py command line option
filter-abund.py command line option
normalize-by-median.py command line option
trim-low-abund.py command line option
-d
extract-paired-reads.py command line option
split-paired-reads.py command line option
-e
unique-kmers.py command line option
-f
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
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
-k
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
-l
extract-long-sequences.py command line option
normalize-by-median.py command line option
trim-low-abund.py command line option
-M
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
sample-reads-randomly.py command line option
trim-low-abund.py command line option
-m
extract-partitions.py command line option
-N
sample-reads-randomly.py command line option
-n
extract-partitions.py command line option
fastq-to-fasta.py command line option
load-graph.py command line option
-o
extract-long-sequences.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
readstats.py command line option
sample-reads-randomly.py command line option
trim-low-abund.py command line option
-p
extract-paired-reads.py command line option
normalize-by-median.py command line option
-q
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
normalize-by-median.py command line option
sample-reads-randomly.py command line option
unique-kmers.py command line option
-S
make-initial-stoptags.py command line option
partition-graph.py command line option
sample-reads-randomly.py command line option
unique-kmers.py command line option
-s
abundance-dist-single.py command line option
abundance-dist.py command line option
do-partition.py command line option
extract-paired-reads.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
partition-graph.py command line option
trim-low-abund.py command line option
-T
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-low-abund.py command line option
-U
abundance-dist-single.py command line option
do-partition.py command line option
extract-partitions.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
normalize-by-median.py command line option
-V
filter-abund-single.py command line option
filter-abund.py command line option
trim-low-abund.py command line option
-X
extract-partitions.py command line option
-Z
filter-abund-single.py command line option
filter-abund.py command line option
trim-low-abund.py command line option
-z
abundance-dist-single.py command line option
abundance-dist.py command line option
A
abundance-dist-single.py command line option
--force
--fp-rate
--help
--info
--ksize
--max-memory-usage
--no-bigcount
--no-zero
--quiet
--savegraph
--small-count
--squash
--threads
--unique-kmers
--version
-b
-f
-h
-k
-M
-q
-s
-T
-U
-z
input_sequence_filename
output_histogram_filename
abundance-dist.py command line option
--force
--help
--info
--no-bigcount
--no-zero
--quiet
--squash
--version
-b
-f
-h
-q
-s
-z
input_count_graph_filename
input_sequence_filename
output_histogram_filename
annotate-partitions.py command line option
--force
--help
--info
--ksize
--version
-f
-h
-k
graphbase
input_sequence_filename
B
basename
partition-graph.py command line option
C
count-median.py command line option
--force
--help
--info
--version
-f
-h
input_count_graph_filename
input_sequence_filename
output_summary_filename
D
do-partition.py command line option
--force
--fp-rate
--help
--info
--keep-subsets
--ksize
--max-memory-usage
--no-big-traverse
--subset-size
--threads
--unique-kmers
--version
-f
-h
-k
-M
-s
-T
-U
graphbase
input_sequence_filename
E
extract-long-sequences.py command line option
--bzip
--gzip
--help
--info
--length
--output
--version
-h
-l
-o
input_filenames
extract-paired-reads.py command line option
--bzip
--force
--gzip
--help
--info
--output-dir
--output-paired
--output-single
--version
-d
-f
-h
-p
-s
infile
extract-partitions.py command line option
--bzip
--force
--gzip
--help
--info
--max-size
--min-partition-size
--no-output-groups
--output-unassigned
--version
-f
-h
-m
-n
-U
-X
input_partition_filename
output_filename_prefix
F
fastq-to-fasta.py command line option
--bzip
--gzip
--help
--info
--n_keep
--output
--version
-h
-n
-o
input_sequence
filenames
readstats.py command line option
sample-reads-randomly.py command line option
filter-abund-single.py command line option
--bzip
--cutoff
--force
--fp-rate
--gzip
--help
--info
--ksize
--max-memory-usage
--normalize-to
--outfile
--quiet
--savegraph
--small-count
--threads
--unique-kmers
--variable-coverage
--version
-C
-f
-h
-k
-M
-o
-q
-T
-U
-V
-Z
input_sequence_filename
filter-abund.py command line option
--bzip
--cutoff
--force
--gzip
--help
--info
--normalize-to
--output
--quiet
--threads
--variable-coverage
--version
-C
-f
-h
-o
-q
-T
-V
-Z
input_count_graph_filename
input_sequence_filename
filter-stoptags.py command line option
--force
--help
--info
--ksize
--version
-f
-h
-k
input_sequence_filename
input_stoptags_filename
find-knots.py command line option
--force
--fp-rate
--help
--info
--ksize
--max-memory-usage
--small-count
--unique-kmers
--version
-f
-h
-k
-M
-U
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
--force
--gzip
--help
--info
--no-reformat
--output
--version
-f
-h
-o
left
right
L
left
interleave-reads.py command line option
load-graph.py command line option
--force
--fp-rate
--help
--info
--ksize
--max-memory-usage
--no-build-tagset
--threads
--unique-kmers
--version
-f
-h
-k
-M
-n
-T
-U
input_sequence_filename
output_nodegraph_filename
load-into-counting.py command line option
--force
--fp-rate
--help
--info
--ksize
--max-memory-usage
--no-bigcount
--quiet
--small-count
--summary-info
--threads
--unique-kmers
--version
-b
-f
-h
-k
-M
-q
-s
-T
-U
input_sequence_filename
output_countgraph_filename
M
make-initial-stoptags.py command line option
--force
--fp-rate
--help
--info
--ksize
--max-memory-usage
--small-count
--stoptags
--subset-size
--unique-kmers
--version
-f
-h
-k
-M
-s
-S
-U
graphbase
merge-partition.py command line option
--force
--help
--info
--keep-subsets
--ksize
--version
-f
-h
-k
graphbase
N
normalize-by-median.py command line option
--bzip
--cutoff
--force
--force_single
--fp-rate
--gzip
--help
--info
--ksize
--loadgraph
--max-memory-usage
--output
--paired
--quiet
--report
--report-frequency
--savegraph
--small-count
--unique-kmers
--unpaired-reads
--version
-C
-f
-h
-k
-l
-M
-o
-p
-q
-R
-s
-U
-u
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
--force
--help
--info
--no-big-traverse
--stoptags
--subset-size
--threads
--version
-f
-h
-S
-s
-T
basename
R
readstats.py command line option
--csv
--help
--info
--output
--version
-h
-o
filenames
right
interleave-reads.py command line option
S
sample-reads-randomly.py command line option
--bzip
--force
--force_single
--gzip
--help
--info
--max_reads
--num_reads
--output
--random-seed
--samples
--version
-f
-h
-M
-N
-o
-R
-S
filenames
split-paired-reads.py command line option
--bzip
--force
--gzip
--help
--info
--output-dir
--output-first
--output-orphaned
--output-second
--version
-0
-1
-2
-d
-f
-h
infile
T
trim-low-abund.py command line option
--bzip
--cutoff
--diginorm
--diginorm-coverage
--force
--fp-rate
--gzip
--help
--ignore-pairs
--info
--ksize
--loadgraph
--max-memory-usage
--normalize-to
--output
--quiet
--savegraph
--single-pass
--small-count
--summary-info
--tempdir
--trim-at-coverage
--unique-kmers
--variable-coverage
--version
-C
-h
-k
-l
-M
-o
-q
-s
-T
-U
-V
-Z
input_filenames
U
unique-kmers.py command line option
--diagnostics
--error-rate
--help
--info
--ksize
--quiet
--report
--stream-records
--version
-e
-h
-k
-q
-R
-S
input_sequence_filename
Navigation
index
khmer 3.0.0~a3+dfsg-7 documentation
»
Index