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Usage
Denis Verkhoturov edited this page Apr 22, 2019
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java -jar metamer.jar [-h | --help] [-k <number> <-f | --format> <format> <-i | --input> <path> <-o | --output> <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 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