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https://github.com/cumbof/minimizers

A Python package for extracting minimizers from sequence data
https://github.com/cumbof/minimizers

fasta genome minimizer sketch

Last synced: 26 days ago
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A Python package for extracting minimizers from sequence data

Host: GitHub
URL: https://github.com/cumbof/minimizers
Owner: cumbof
License: mit
Created: 2023-04-21T17:30:42.000Z (over 1 year ago)
Default Branch: main
Last Pushed: 2023-04-26T03:48:30.000Z (over 1 year ago)
Last Synced: 2024-11-16T09:48:37.179Z (about 1 month ago)
Topics: fasta, genome, minimizer, sketch
Language: Python
Homepage:
Size: 9.77 KB
Stars: 0
Watchers: 1
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

# 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](https://pypi.org/project/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
```