Metamer

Genome assembler de novo that uses De Bruijn graph.

Table of Contents

• Install
  • Dependencies
• Usage
  • Options
  • Examples
    • General use cases
    • Pipeline mode
• Maintainer
• Contributing
  • Contributors
• License

Install

Please, visit the releases page to download the tool.

Dependencies

• Java 11

Usage

java -jar metamer.jar [-h | --help] [-k <number> -f <format> -i <path> -o <path>]

Options

-h, --help - show usage.

-k - the length of k that will be used to build De Bruijn graph.

-f, --format - the format of input data that will be used to read records, can be one of: fasta, fastq.

-i, --input - input file with reads to be analyzed.

-o, --output - output file to write the result to.

Examples

General use cases

Use Fasta file as input:

java -jar metamer.jar -k 42 -f fasta -i ~/path/to/input.fasta -o ~/path/to/output.fasta

Use FastQ file as input:

java -jar metamer.jar -k 42 -f fastq -i ~/path/to/input.fastq -o ~/path/to/output.fasta

Pipeline mode

For all examples below used fasta format but it can be used with fastq in the exact same way as well.

Read from stdin and write to stdout:

java -jar metamer.jar -k 42 -f fasta

Read from file and write to stdout:

java -jar metamer.jar -k 42 -f fasta -i ~/path/to/input.fasta

Read from stdin and write to a file:

java -jar metamer.jar -k 42 -f fasta -o ~/path/to/output.fasta

Maintainer

Denis Verkhoturov

Contributing

Issues and pull-requests are appreciated, thank you for paying attention to project Metamer! Please take a look at our code of conduct and contributing guide.

Contributors

• Aleksandra Klimina
• Anna Brusnitsyna
• Denis Verkhoturov
• Irina Shapovalova
• Sophia Shalgueva

License

This project is licenced under the terms of the MIT license.