minimizers

A Python package for extracting minimizers from sequence data.

Requirements

The package requires Python 3 and there are no constraints on the type of operating system.

It also requires the biopython package.

Install

It can be installed with pip by typing the following command in your terminal:

pip install minimizers

How to use it

Run minimizers --help for a list of available arguments:

usage: minimizers [-h] [-a] -i INPUT [-o OUTPUT] [-t {list,fasta}] -s SIZE -w
                  WINDOW [--report-counts] [--top-perc TOP_PERC]
                  [--top-num TOP_NUM] [-n NPROC] [--verbose] [-v]

Extract the set of minimizers from a sequence file

optional arguments:
  -h, --help            show this help message and exit
  -a, --aggregate       Aggregate record results (default: False)
  -i INPUT, --input INPUT
                        Path to the input sequence file in fasta format. It
                        can be Gzip compressed (default: None)
  -o OUTPUT, --output OUTPUT
                        Path to the output file with minimizers. Results are
                        printed on the stdout if no output is provided
                        (default: None)
  -t {list,fasta}, --output-type {list,fasta}
                        The output can be formatted as a list of kmers or as a
                        fasta file (default: list)
  -s SIZE, --size SIZE  Length of the minimizers (default: None)
  -w WINDOW, --window WINDOW
                        Size of the sliding window. It must be greater than
                        the minimizer size (default: None)
  --report-counts       Report the frequencies of the minimizers. This is
                        compatible with "--output-type list" only (default:
                        False)
  --top-perc TOP_PERC   Report the top percentage of minimizers based on their
                        frequency (default: None)
  --top-num TOP_NUM     Report the top number of minimizers based on their
                        frequency (default: None)
  -n NPROC, --nproc NPROC
                        Make it parallel (default: 1)
  --verbose             Print messages on the stdout (default: False)
  -v, --version         Print the "minimizers" version and exit

Copyright © 2022 Fabio Cumbo. See LICENSE for additional details.