{ "info": { "author": "Robert Leach, Lance Parsons", "author_email": "rleach@princeton.edu, lparsons@princeton.edu", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.1", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "================\nBarcode Splitter\n================\nA utility to split multiple sequence files using multiple sets of barcodes.\n\nCopyright 2017 Lance Parsons , Robert Leach \n\n`BSD 2-Clause License `_ - See ``LICENSE.txt``\n\nInstallation\n============\n1. Install Barcode Splitter::\n\n pip install barcode_splitter\n\n\nbarcode_splitter\n================\n\nSplit multiple fastq files by matching barcodes in one or more of the sequence\nfiles. Barcodes in the tab-delimited ``barcodes.txt`` file are matched against\nthe beginning (or end) of the specified index read(s). By default, barcodes must\nmatch exactly, but ``--mistmatches`` can be set higher if desired. Compressed\ninput is read (from all files) if the first input file name ends in ``.gz``.\nReading of compressed input can be forced with the ``gzipin`` option.\n\nExamples\n--------\n\nSplit an Illumina paired-end run where the index read are in the second read\nfile (read 2), the forward read is the first read file (read 1), and the reverse\nreads are in the third read file (read 3)::\n\n barcode_splitter --bcfile barcodes.txt read1.fastq read2_index.fastq read3.fastq --idxread 2 --suffix .fastq\n\nUTF-8\n-----\n\nSample names containing UTF-8 characters are allowed, however, outputting those\ncharacters to STDOUT and piping to a file can be problematic. Ensure python\nuses the proper encoding for STDOUT by setting ``PYTHONIOENCODING='utf-8'``.::\n\n PYTHONIOENCODING='utf-8' barcode_splitter --bcfile barcodes_utf8.txt read1.fastq read2_index.fastq read3.fastq --idxread 2 --suffix .fastq\n\n\nCitation\n========\n\nPlease use the following `BibTeX `_ entry::\n\n @misc{leach_bcs_2019,\n address = {Princeton, {NJ}, {USA}},\n title = {Barcode Splitter, version 0.18.5 [Software]},\n url = {https://bitbucket.org/princeton_genomics/barcode_splitter},\n author = {Leach, Robert and\n Parsons, Lance},\n year = {2019}\n }\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://bitbucket.org/princeton_genomics/barcode_splitter", "keywords": "sequencing fastq paired barcode demultiplex", "license": "BSD 2-clause", "maintainer": "", "maintainer_email": "", "name": "barcode-splitter", "package_url": 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