Provided by: mash_2.0-2ubuntu2_amd64
mash-dist - estimate the distance of query sequences to references
mash dist [options] <reference> <query> [<query>] ...
Estimate the distance of each query sequence to the reference. Both the reference and queries can be fasta or fastq, gzipped or not, or Mash sketch files (.msh) with matching k-mer sizes. Query files can also be files of file names (see -l). Whole files are compared by default (see -i). The output fields are [reference-ID, query-ID, distance, p-value, shared-hashes].
-h Help -p <int> Parallelism. This many threads will be spawned for processing.  Input -l List input. Each query file contains a list of sequence files, one per line. The reference file is not affected. Output -t Table output (will not report p-values, but fields will be blank if they do not meet the p-value threshold). -v <num> Maximum p-value to report. (0-1) [1.0] -d <num> Maximum distance to report. (0-1) [1.0] Sketching -k <int> K-mer size. Hashes will be based on strings of this many nucleotides. Canonical nucleotides are used by default (see Alphabet options below). (1-32)  -s <int> Sketch size. Each sketch will have at most this many non-redundant min-hashes.  -i Sketch individual sequences, rather than whole files. -w <num> Probability threshold for warning about low k-mer size. (0-1) [0.01] -r Input is a read set. See Reads options below. Incompatible with -i. Sketching (reads) -b <size> Use a Bloom filter of this size (raw bytes or with K/M/G/T) to filter out unique k-mers. This is useful if exact filtering with -m uses too much memory. However, some unique k-mers may pass erroneously, and copies cannot be counted beyond 2. Implies -r. -m <int> Minimum copies of each k-mer required to pass noise filter for reads. Implies -r.  -c <num> Target coverage. Sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity). Implies -r. -g <size> Genome size. If specified, will be used for p-value calculation instead of an estimated size from k-mer content. Implies -r. Sketching (alphabet) -n Preserve strand (by default, strand is ignored by using canonical DNA k-mers, which are alphabetical minima of forward-reverse pairs). Implied if an alphabet is specified with -a or -z. -a Use amino acid alphabet (A-Z, except BJOUXZ). Implies -n, -k 9. -z <text> Alphabet to base hashes on (case ignored by default; see -Z). K-mers with other characters will be ignored. Implies -n. -Z Preserve case in k-mers and alphabet (case is ignored by default). Sequence letters whose case is not in the current alphabet will be skipped when sketching.