| Value | Meaning |
|---|---|
| numberOfThreads"-t" | number of threads (default 4) |
| windowSize"-w" | window size (default 40) |
| advanceSize"-a" | advance size (default 10) |
| maxDepth"-d" | max depth (default 18446744073709551615) |
| produceFullSequences"-f" | produce full sequences (default 0) |
| verbosity"-V" | verbosity (default 18446744073709551615) |
| readInterval"-I" | read interval (default 0,18446744073709551615) |
| readsPart"-J" | reads part (default 0,1) |
| errorProfileFileName"-E" | error profile file name (default input.las.eprof) |
| minWindowCoverage"-m" | minimum window coverage (default 3) |
| maxWindowError"-e" | maximum window error (default 18446744073709551615) |
| minLengthOfOutput"-l" | minimum length of output (default 0) |
| minKMerFilterFrequency"--minfilterfreq" | minimum k-mer filter frequency (default 0) |
| maxKMerFilterFrequency"--maxfilterfreq" | maximum k-mer filter frequency (default 2) |
| temporaryFilePrefix"-T" | temporary file prefix (default daccord_ozelot_4500_1529654843) |
| maxAlignmentsPerRead"-D" | maximum number of alignments considered per read (default 5000) |
| maxAlignmentsPerReadVard"--vard" | maximum number of alignments considered per read (default 0) |
| computeErrorProfileOnly"--eprofonly" | compute error profile only (default disable) |
| computeErrorDistributionEstimate"--deepprofileonly" | compute error distribution estimate (default disable) |
| kmerSize"-k" | kmer size (default 8) |
Options for daccord.