{ "info": { "author": "Richard Jovelin", "author_email": "richard.jovelin@oicr.on.ca", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: MacOS", "Operating System :: POSIX", "Operating System :: Unix", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering", "Topic :: Software Development" ], "description": "Debarcer\n========\n\nA package for De-Barcoding and Error Correction of sequencing data containing molecular barcodes. For information on getting started with Debarcer, see the `Installation Guide`_.\n\n.. _`Installation Guide`: https://github.com/oicr-gsi/debarcer/wiki/1.-Installation-Guide\n\nNote : The repository for the original release of Debarcer (V0.3.1) as described in Nature Protocols can be found under \nhttps://github.com/oicr-gsi/debarcer/releases/tag/v0.3.1 \n\nhttps://github.com/oicr-gsi/debarcer/tree/master-old\n\n\nConfiguration\n-------------\n\nA sample config file is provided in ``/debarcer/config/sample_config.ini``, and a sample prepfile is provided in ``/debarcer/config/library_prep_types.ini``. Thresholds and paths that you expect to use multiple times should be stored in the config file. The prepfile contains instructions for how different library preps should be handled, for example:\n\n.. code:: ini\n\n\t; One library entry\n\t[LIBRARY_NAME]\n\tINPUT_READS=3\n\tOUTPUT_READS=2\n\tUMI_LOCS=2\n\tUMI_LENS=10\n\tSPACER=FALSE\n\n* INPUT_READS:\n\tNumber of unprocessed fastq files (1-3).\n* OUTPUT_READS:\n\tNumber of fastq files after reheadering (1-2).\n* UMI_LOCS:\n\tComma-separated indices of reads containing a UMI (1-3).\n* UMI_LENS:\n\tComma-separated lengths of UMIs corresponding to UMI_LOCS (1-100).\n* SPACER:\n\tTRUE if a spacer is present, FALSE otherwise (TRUE/FALSE).\n* SPACER_SEQ (optional):\n\tBase sequence of the spacer ([A,C,G,T]+).\n\n``LIBRARY_NAME`` would then be the ``--prepname`` argument passed to debarcer.py.\n\nTypical Workflow\n----------------\n\n.. code:: bash\n\n\t## Preprocess some fastq files\n\t$ python debarcer.py preprocess -o /path/to/output_dir -r1 /path/to/read1.fastq -r2 /path/to/read2.fastq\n\t -prepname \"prepname\" -prepfile /path/to/library_prep_types.ini\n\n\t## Align, sort, index\n\t## ...\n\t## produces: bam_file.bam, bam_file.bam.bai\n\n\t## Error-correct and group UMIs into families\n\t$ python debarcer.py group -r chrN:posA-posB -c /path/to/config.ini -b /path/to/bam_file.bam\n\t -o /path/to/output_dir\n\n\t## Perform base collapsing\n\t$ python debarcer.py collapse -o /path/to/output_dir -r chrN:posA-posB\n -b /path/to/bam_file.bam -u /path/to/umi_file.umis\n -c /path/to/config.ini\n\n\t## Call variants of specified family sizes\n $ python debarcer.py call -o /path/to/output_dir -r chrN:posA-posB\n -cf /path/to/cons_file.cons -f 1,2,5 -c path/to/config.ini\n\nDependencies\n------------\n\nDebarcer was tested using Python 3.6.4 and depends on the packages pysam and pandas. 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