Provided by: mash_2.0-2ubuntu2_amd64 bug


       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].



       -p <int>
           Parallelism. This many threads will be spawned for processing. [1]

           List input. Each query file contains a list of sequence files, one per line. The
           reference file is not affected.

           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]

       -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) [21]

       -s <int>
           Sketch size. Each sketch will have at most this many non-redundant min-hashes. [1000]

           Sketch individual sequences, rather than whole files.

       -w <num>
           Probability threshold for warning about low k-mer size. (0-1) [0.01]

           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. [1]

       -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)
           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.

           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.

           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.