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