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mash sketch (version 2.3+galaxy0)

Input: Reads or Assemblies:

Single or Paired-end reads:

Select between paired and single end data

Select first set of reads:

Specify dataset with forward reads

Select second set of reads:

Specify dataset with reverse reads

Minimum copies of each k-mer required to pass noise filter:

Target coverage:

If specified, sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity)

Genome size:

If specified, will be used for p-value calculation instead of an estimated size from k-mer content

Sketch size:

Each sketch will have at most this many non-redundant min-hashes

kmer size:

Probability threshold for warning about low k-mer size:

What it does

Create a sketch file, which is a reduced representation of a sequence or set of sequences (based on min-hashes) that can be used for fast distance estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can be given to read from standard input. Input files can also be files of file names (see -l). For output, one sketch file will be generated, but it can have multiple sketches within it, divided by sequences or files (see -i). By default, the output file name will be the first input file with a '.msh' extension, or 'stdin.msh' if standard input is used (see -o).