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Denis Verkhoturov edited this page Apr 22, 2019 · 3 revisions

Usage

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