Command Line Options¶
meryl2 Global Options¶
In meryl2, global options apply to every action. Global options are expressed as command line switches. K-mer size, label size, memory usage, number of threads, and simple sequence reductions are all global options.
Processing is specified as a list of actions
and are described elsewhere.
1KMER and LABEL SIZE:
2 -k K Set kmer size to K (6 <= K <= 64). Legacy format "k=K".
3 -l L Set label size to L bits (0 <= L <= 64).
4
5SIMPLE SEQUENCE REDUCTION:
6 --compress Homopolymer compress input sequence before forming kmers.
7 --ssr ssr-spec Apply 'ssr-spec' to input sequence before forming kmers.
8
9RESOURCE USAGE:
10 -m M Use up to M GB memory for counting. Legacy format "memory=M".
11 --memory M Use up to M GB memory for counting.
12
13 -t T Use T threads for counting and processing.
14 --threads T Use T threads for counting and processing.
15
16LOGGING:
17 -V[V[V[...]]] Increae verbosity by the length of this option.
18 -Q Be absolutely silent.
19 -P Show progress.
20 -C Show processing tree and stop.
21
22USAGE:
23 -h Display command line help.
24 --help Display command line help.
25 help Display command line help.
Obsolete forms of some of these are still allowed. The kmer size can be set with k=<kmer-size>, memory limits with memory=<memory-in-gigabytes>, thread usage with threads=<thread-count>.
Obsolete option -E has been removed. This used to estimate the size of an imput that could be counted in some given memory size.
1dumpIndex <meryl-database>
2 Report the parameters used for storing data in this meryl database.
3
4dumpFile <meryl-database-file>
5 Dump the raw data from a merylData file in a meryl database.
meryl2-lookup Usage¶
1usage: meryl2-lookup <report-type> \
2 -sequence <input1.fasta> [<input2.fasta>] \
3 -output <output1> [<output2>] \
4 -mers <input1.meryl> [<input2.meryl>] [...] [-estimate] \
5 -labels <input1name> [<input2name>] [...]
6
7 Compare kmers in input sequences against kmers in input meryl databases.
8
9 Input sequences (-sequence) can be FASTA or FASTQ, uncompressed, or
10 compressed with gzip, xz, or bzip2.
11
12 Report types:
13
14 -bed:
15 Generate a BED format file showing the location of kmers in
16 any input database on each sequence in 'input1.fasta'.
17 Each kmer is reported in a separate bed record.
18
19 -bed-runs:
20 Generate a BED format file showing the location of kmers in
21 any input database on each sequence in 'input1.fasta'.
22 Overlapping kmers are combined into a single bed record.
23
24 -wig-count:
25 Generate a WIGGLE format file showing the multiplicity of the
26 kmer starting at each position in the sequence, if it exists in
27 an input kmer database.
28
29 -wig-depth:
30 Generate a WIGGLE format file showing the number of kmers in
31 any input database that cover each position in the sequence.
32
33 -existence:
34 Generate a tab-delimited line for each input sequence with the
35 number of kmers in the sequence, in the database and common to both.
36
37 -include:
38 -exclude:
39 Copy sequences from 'input1.fasta' (and 'input2.fasta') to the
40 corresponding output file if the sequence has at least one kmer
41 present (include) or no kmers present (exclude) in 'input1.meryl'.
42
43Run `meryl2-lookup <report-type> -help` for details on each method.