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        "author": "Alastair Maxwell/University of Glasgow",
        "author_email": "alastair.maxwell@glasgow.ac.uk",
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            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
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        "description": "ScaleHD-ALSPAC: Automated Huntington Disease genotyping with end-to-end allele masking\n======================================================================================\n\n!! You probably don't want to use this version of ScaleHD, unless you know what you're doing. Use the vanilla version, instead. !!\n\nScaleHD-ALSPAC is a package for automating the process of genotyping microsatellite repeats in Huntington Disease data.\nWe utilise machine learning approaches to take into account natural data 'artefacts', such as PCR slippage and somatic\nmosaicism, when processing data. This provides the end-user with a simple to use platform which can robustly predict genotypes from input data.\n\nBy default, input is a pair of unaligned .fastq sequence data -- both forward and reverse reads, per sample. We utilise both forward and reverse\nreads in order to reduce the complex dimensionality issue posed by Huntington Disease's multiple repeat tract genetic structure. Reverse reads allow\nus to determine the current sample's CCG state -- this provides us with a mechanism by which to more easily call the entire genotype. Forward reads\nare utilised in a similar approach, to determine the CAG and intervening structure.\n\nThe general overview of the application is as follows:\n1) Input FastQ files are subsampled, if an overwhelming number of reads are present. This can be overruled with the -b flag.\n2) Sequence quality control is carried out per the user's instructions. We reccomend trimming of any 5-prime spacer+primer combinations, for optimal alignment.\n3) Alignment of these files, to a typical HD structure (CAG_1_1_CCG_2) reference, is carried out.\n4) Assemblies are scanned with Digital Signal Processing to detect any possible atypical structures (e.g. CAG_2_1_CCG_3).\n4.1) If no atypical alleles are detected, proceed as normal.\n4.2) If atypical alleles are detected, a custom reference is generated, and re-alignment to this is carried out.\n5) With the appropriate allele information and sequence assembly(ies) present, sampled are genotyped.\n6) Output is written for the current sample; the procedure is repeated for the next sample in the queue (if present).\n\n\nCheck the full documentation at http://scalehd.rtfd.io",
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        "keywords": "machine-learning genotyping bioinformatics huntington-disease",
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        "name": "ScaleHDALSPAC",
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