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        "author": "Hadrien Gourl\u00e9, Renaud Van Damme",
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        "description": "# The Capture-Seq assembler\n\n[![Build Status](https://travis-ci.org/SGBC/capture.svg?branch=master)](https://travis-ci.org/SGBC/capture)\n[![made-with-python](https://img.shields.io/badge/made%20with-python3-blue.svg)](https://www.python.org/)\n[![LICENSE](https://img.shields.io/badge/license-MIT-lightgrey.svg)](https://github.com/SGBC/capture)\n\n`capture` is an assembler developed to recover complete genome from ultra-high coverage samples\n\nThe repository is a work in progress and the assembler is not functional yet.\nThanks for your interest and come back soon!\n\n## Installation\n\n`capture` requires the following to be installed:\n\n* python >= 3.6\n* SPAdes\n\n*TODO*\n\n## Quickstart\n\n```bash\n# paired-end reads, Illumina MiSeq\ncapture assemble -f reads_R1.fastq.gz -r reads_R2.fastq.gz \\\n--genome_size 35000 --mean 300 -o output_dir\n# compressed paired-end reads, Illumina HiSeq\ncapture assemble -f reads_R1.fastq.gz -r reads_R2.fastq.gz \\\n--genome_size 35000 --mean 125 -o output_dir\n# single end reads, Ion Torrent\ncapture assemble -u reads.fastq.gz \\\n--genome_size 35000 --mean 240 -o output_dir\n# reads in bam format\ncapture assemble --bam reads.bam \\\n--genome_size 35000 --mean 240 -o output_dir\n# full list of subcommands and options\ncapture -h\n# full list of options for a subcommand\ncapture assemble -h\n```\n\n## License\n\nCode is under the [MIT](LICENSE) license\n\n## Contributing\n\nWe welcome contributions from the community! See our [Contributing](CONTRIBUTING.md) guide.\n\n\n",
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