Genome assembler de novo that uses De Bruijn graph.
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
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.
This project is licenced under the terms of the MIT license.