Genome assembler de novo that uses De Bruijn graph.

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

Please, visit the releases page to download the tool.

• Java 11

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

-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.

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

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

Denis Verkhoturov

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.

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

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