NAME

       mash-dist - estimate the distance of query sequences to references

SYNOPSIS

       mash dist [options] <reference> <query> [<query>] ...

DESCRIPTION

       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].

OPTIONS

       -h
           Help

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

   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) [21]

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

       -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. [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)
       -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.

SEE ALSO

       mash(1)

                                            2019-12-13                               MASH-DIST(1)