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        "author": "Matthew Wakefield",
        "author_email": "matthew.wakefield@unimelb.edu.au",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "Experimental Alpha Release of AmBiVErT\n--------------------------------------\n\nThis program is designed for the processing of amplicon based resequencing data\ngenerated on second generation sequencing platforms (eg Illumina HiSeq/MiSeq).\n\nThe approach used is to batch reads derived from each amplicon together in a\nclustering step prior to aligning the sequence to a reference genome.\n\nSteps:\n    1)  Cluster similar reads\n    2)  Align for overlap\n    3)  Align to reference target sequences\n    4)  Consolidate calls\n    5)  Output VCF format calls\n\n\nCreated by Matthew Wakefield and Graham Taylor.\nCopyright (c) 2013  Matthew Wakefield and The University of Melbourne. All rights reserved.\n\n$ ambivert --help\nusage: ambivert [-h] [-f FORWARD] [-r REVERSE] [-m MANIFEST] [--fasta FASTA]\n                [--output OUTPUT] [--countfile COUNTFILE]\n                [--threshold THRESHOLD] [--min_cover MIN_COVER]\n                [--min_reads MIN_READS] [--min_freq MIN_FREQ]\n                [--overlap OVERLAP] [--hashtable HASHTABLE]\n                [--savehashtable SAVEHASHTABLE] [--alignments ALIGNMENTS]\n                [--prefix PREFIX]\n\nAmBiVErT: A program for binned analysis of amplicon data AmBiVErT clusters\nidentical amplicon sequences and thresholds based on read frequency to remove\ntechnical errors. Due to sequencing errors occuring with a more random\ndistribution than low frequency variants this approach reduces the number of\namplicon products that must be assigned to target regions & assessed for\nvariant calls. AmBiVErT overlaps forward and reverse reads from the same\namplicon and preserves local phasing information. Typical running time for\nfirst use is several hours, which reduces to less than 10 minutes when the\nhash table calculated on a previous run is supplied for analysis of subsequent\nsamples with the same amplicons.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -f FORWARD, --forward FORWARD\n                        a fastq format file of forward direction amplicon\n                        reads. May be compressed with gzip with the\n                        appropriate suffix (.gz)\n  -r REVERSE, --reverse REVERSE\n                        a fastq format file of reverse direction amplicon\n                        reads. May be compressed with gzip with the\n                        appropriate suffix (.gz)\n  -m MANIFEST, --manifest MANIFEST\n                        an Illumina TrueSeq Amplicon manifest file.\n  --fasta FASTA         an fasta amplicon manifest file. Sequences should be\n                        limited to the regions to be called and exclude\n                        primers & adaptors. This file can be provided in\n                        addition to an Illumina manifest to specify additional\n                        off target regions.\n  --output OUTPUT       output of alignments with variants. Default: stdout\n  --countfile COUNTFILE\n                        output of occurance counts per amplicon. Includes all\n                        counts that map to the reference amplicon. This count\n                        does not include reads that occured at frequencies\n                        below --threshold <default=20>\n  --threshold THRESHOLD\n                        the minimum occurance threshold. Unique amplicon\n                        sequence variants that occur fewer than threshold\n                        times are ignored. Default 20\n  --min_cover MIN_COVER\n                        the minimum coverage at a site required to call a\n                        variant. This parameter only has effect if it is >\n                        threshold. Default 0\n  --min_reads MIN_READS\n                        the minimum number of variant containing reads\n                        required to call a variant. This parameter only has\n                        effect if it is > threshold. Default 0\n  --min_freq MIN_FREQ   the minimum proportion of mutated reads. Default 0.1\n                        (ten percent)\n  --overlap OVERLAP     The minimum overlap required between forward and\n                        reverse sequences to merge. Default 20bp\n  --hashtable HASHTABLE\n                        Filename for a precomputed hash table of exact matches\n                        of amplicons to references. Generate with\n                        --savehashtable\n  --savehashtable SAVEHASHTABLE\n                        Output a precomputed hash table that matches amplicons\n                        exactly to references. Used to speed up matching with\n                        --hashtable\n  --alignments ALIGNMENTS\n                        Print a formatted text version of variant containing\n                        alignments to a file. \"-\" will print to stderr\n  --prefix PREFIX       Shorthand specification of --forward, --reverse,\n                        --countfile and --outfile. --forward =\n                        <prefix>_R1.fastq.gz --reverse = <prefix>_R2.fastq.gz\n                        --outfile = <prefix>.vcf --countfile = <prefix>.counts\n\t\t\t\t\t\t\n\t\t\t\t\t\t\nAdditional tools for simulating amplicon data\n---------------------------------------------\n\nsimulate_variants\n------------------\n\nusage: simulate_variants [-h] [--manifest MANIFEST] [--fasta FASTA]\n                         [--read1 READ1] [--read2 READ2] [--skip_softmasked]\n                         [--position_excludes_softmasked]\n                         [--deletions DELETIONS] [--check_sam CHECK_SAM]\n\nA script for simulating paired end reads with variants from an amplicon target\nfile\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --manifest MANIFEST   an Illumina TrueSeq Amplicon manifest file. Default:\n                        None\n  --fasta FASTA         a fasta file of amplicons all in the plus strand\n                        orientation with description lines \">name chromosome\n                        start end\" Default: None\n  --read1 READ1         a fastq output file of forward reads. Default: stdout\n  --read2 READ2         a fastq output file of reverse reads. Default: stdout\n  --skip_softmasked     dont generate variants in softmasked sequence.\n                        Default: True\n  --position_excludes_softmasked\n                        Exclude softmasked sequence when calculating start\n                        site of read, cigar and variant detection strings.\n                        Default: True\n  --deletions DELETIONS\n                        The size deletions to insert instead of point\n                        variants. Default: None\n  --check_sam CHECK_SAM\n                        a sam file for parsing to identify entries where name\n                        does not match the sam file mapping location and\n                        variant strings\n\ntruseq_manifest\n---------------\n\nusage: truseq_manifest [-h] [--manifest MANIFEST] [--output OUTPUT] [--probes]\n                       [--adaptors] [--with_probes] [--softmask_probes]\n                       [--all_plus]\n\nA script for converting Illumina TruSeq Amplicon manifest files to fasta files\nProduces either a fasta file of target sequences without primers or a file of\nprimer sequences suitable for use by a trimming program (eg Nesoni clip)\n\noptional arguments:\n  -h, --help           show this help message and exit\n  --manifest MANIFEST  an Illumina TruSeq Amplicon manifest file. Default:\n                       stdin\n  --output OUTPUT      a multi fasta output file of sequence targets. Default:\n                       stdout\n  --probes             output only the ULSO and DLSO primer sequences\n  --adaptors           append Illumina adaptor sequences to the primer\n                       sequences\n  --with_probes        append the ULSO and DLSO sequences to the fasta target\n                       sequences\n  --softmask_probes    append the ULSO and DLSO sequences to the fasta target\n                       sequences\n  --all_plus           reorient target sequences so they are all presented on\n                       the plus strand",
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        "summary": "AmBiVErT - AMplicon BInning Variant caller with ERror Truncation.                 For calling variants in amplicon based sequencing experiments",
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