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Add first 5k reads from the proc. benchmark as an small example set
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milot-mirdita committed Aug 8, 2018
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4 changes: 2 additions & 2 deletions README.md
Expand Up @@ -22,7 +22,7 @@ The following command will download the last Plass version, extract it and set t
Plass can assemble both paired-end reads (FASTQ) and single reads (FASTA or FASTQ):

# assemble paired-end reads
plass assemble read_1.fastq read_2.fastq assembly.fas tmp
plass assemble reads_1.fastq reads_2.fastq assembly.fas tmp

# assemble single-end reads
plass assemble reads.fasta assembly.fas tmp
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We also provide a Docker image of Plass. You can mount the current directory containing the reads to be assembled and run plass with the following command:

docker pull soedinglab/plass
docker run -ti --rm -v "$(pwd):/app" -w /app plass assemble read_1.fastq read_2.fastq assembly.fas tmp
docker run -ti --rm -v "$(pwd):/app" -w /app plass assemble reads_1.fastq reads_2.fastq assembly.fas tmp

## Hardware requirements
Plass needs roughly 1 byte of memory per residue to work efficiently. Plass will scale its memory consumption based on the available main memory of the machine. Plass needs a CPU with at least the SSE4.1 instruction set to run.
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