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        "description": "# Contig Tools\n## Installation\n```\npip3 install contig-tools\n```\n\n## Usage\n```\nusage: contig-tools [-h] [-v] {filter,metrics,check_metrics} ...\n\nA package to maniuplate and assess contigs arising from de novo assemblies\n\n\npositional arguments:\n  {filter,metrics,check_metrics}\n                        The following commands are available. Type\n                        contig_tools <COMMAND> -h for more help on a specific\n                        commands\n    filter              Filter contigs based on either length and/or coverage\n    metrics             Print contig metrics\n    check_metrics       check contig metrics\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -v, --version         display the version number\n```\n\n## Examples\n**filter contigs**\n```\ncontig-tools filter -l 500 -c 3 -f contigs.fasta\n```\n\n**print contig metrics**\n```\ncontig-tools metrics -f contig_tools/tests/test_data/test.fas\ncontig-tools metrics -f contig_tools/tests/test_data/test.fas -o json\n```\n**check if contigs meet conditions based on conditions enoded in a yaml file**\n\nexample yaml file\n```\nN50 score:\n  condition_type: gt\n  condition_value: 10\nLargest contig:\n  condition_type: gt\n  condition_value: 15\nTotal length:\n  condition_type: lt_gt\n  condition_value:\n    - 100\n    - 50\n```\nexample command\n```\ncontig-tools check_metrics -f contigs.fasta -y conditions.yml\n```\nmetrics that can be checked are\n - Number of contigs\n - Number of contigs > 500bp\n - Total length\n - %GC\n - Largest contig\n - N50 score\n\n conditions that can be used are \n - gt => greater than\n - lt => less than\n - lt_gt => less than and greater than\n\n## code\nCode can be found [here](https://gitlab.com/antunderwood/contig_tools)\n\n",
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