{ "info": { "author": "Mitchell Stanton-Cook", "author_email": "m.stantoncook@gmail.com", "bugtrack_url": null, "classifiers": [], "description": "Banzai\n======\n\nThe Banzai Microbial Genomics Pipeline is currently in closed beta. Please \n`star`_ or `follow`_ this repository to receive updates when it's \npublicly available.\n\n.. _`star`: https://github.com/mscook/Banzai-MicrobialGenomics-Pipeline/star\n\n.. _`follow`: https://github.com/mscook/Banzai-MicrobialGenomics-Pipeline/watchers\n\n\nInstallation\n------------\n\nSee Install.rst_\n\n.. _Install.rst: https://github.com/mscook/Banzai-MicrobialGenomics-Pipeline/blob/master/Install.rst\n\n\nAbout\n-----\n\nBanzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool \ndeveloped within `Dr Scott Beatson's Group`_ at the University of Queensland.\n\n.. _`Dr Scott Beatson's Group`: http://smms-steel.biosci.uq.edu.au\n\nBanzai inherits it's name from the `Banzai 'Pipeline' surf break`_.\n\n.. _`Banzai 'Pipeline' surf break`: http://en.wikipedia.org/wiki/Banzai_Pipeline\n\nBanzai aims to simplify the analysis of large NGS datasets. It has been \nspecifically designed to distribute the workload over internal and external \nHigh Performance Computing (HPC) resources as well as locally available \nworkstations.\n\n\nCore Features\n-------------\n\nBanzai allows for:\n * data validation/quality control of NGS reads,\n * de novo assembly of NGS reads,\n * mapping of NGS reads to reference genomes,\n * ordering of the contigs or scaffolds from draft assemblies against \n reference genomes,\n * phylogenomics tasks (whole genome alignment, SNP based, recombination \n detection)\n * annotating draft assemblies,\n * enrichment of the annotation of draft assemblies,\n * performing common utility tasks like the creation of BLAST databases, \n file format conversion and more.\n\nBanzai supports the NGS platforms that are perdominantly used in Microbial \nGenomics projects.\n\nThe platforms include:\n * `Illumina`_ (single end (SE), paired end (PE) and mate paired (MP)\n reads),\n * `454`_ (SE and PE reads),\n * `ABI SOLiD`_ colorspace reads and\n * `Pacific Biosciences`_ reads (under development)\n\n.. _`Illumina`: http://www.illumina.com/technology/sequencing_technology.ilmn\n.. _`454`: http://www.454.com/\n.. _`ABI SOLiD`: http://www.appliedbiosystems.com.au/\n.. _`Pacific Biosciences`: http://www.pacificbiosciences.com/\n\n**Banzai is by default geared towards 100 bp Illumina Paired End reads.**\n\n\nPhilosophy\n----------\n\nBanzai (in most cases) does not provide new NGS algorithms, it harnesses the \npower of published and tested NGS tools. 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