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.

meryl2 usage.
 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.

meryl2 debugging actions.
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

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.