{"name":"Ragout","tagline":"Ragout - a tool for assisted assembly using multiple references","body":"Ragout (Reference-Assisted Genome Ordering UTility) is a tool for\r\nassisted assembly using multiple references. It takes a short read\r\nassembly (a set of contigs), a set of related references\r\nand a corresponding phylogenetic tree and then assembles the contigs into\r\nscaffolds.\r\n\r\nThe benefits of assembly with multiple references become significant,\r\nwhen those references have structural variations compared to the target\r\ngenome. Even if each reference is structurally divergent, it is possible\r\nto assemble the target into the correct set of scaffolds. Enlarge your\r\ncontigs with Ragout!\r\n\r\nThe current version of Ragout is limited to genomes of bacterial size,\r\nbut we are working on expanding it to mammalian-scaled ones.\r\n\r\nInstallation\r\n------------\r\nLatest version: 0.2 beta (Apr 15 2014)\r\n\r\nThe easiest way to install Ragout is to type:\r\n\r\n    pip install ragout\r\n\r\nYou also can read more detailed _installation instructions_.\r\n\r\nPlease read _manual_.\r\n\r\nAuthors\r\n-------\r\n- Mikhail Kolmogorov (St. Petersburg University of the Russian Academy of\r\nSciences)\r\n- Son Pham (University of California, San Diego)\r\n- Pavel Avdeyev (St. Petersburg University of the Russian Academy of\r\nSciences)\r\n- Dmitry Meleshko (St. Petersburg University of the Russian Academy of\r\nSciences)\r\n\r\nCitation\r\n--------\r\nIf you use Ragout for your research, please cite:\r\n\r\n- Mikhail Kolmogorov, Brian Raney, Benedict Paten, and Son Pham. \r\n\"Ragout: A reference-assisted assembly tool for bacterial genomes\" \r\n(accepted to ISMB 2014)\r\n\r\n\r\nISMB 2014 supplementary\r\n-----------------------\r\n\r\nSupplementary materials for ISMB submission could be found at:\r\nhttps://drive.google.com/file/d/0B1pUguR1yn7TMjNpX09JdFphT3c/edit?usp=sharing\r\n\r\n\r\nContacts\r\n--------\r\nPlease report any bugs directly to the issue tracker of this project.\r\nAlso, you can send your feedback at fenderglass@gmail.com\r\n\r\n\r\nAcknowledgements\r\n----------------\r\nThe work was supported by VP Foundation.\r\n\r\nWe would like to thank:\r\n- Nikolay Vyahhi (testing and some useful suggestions)\r\n- Tamara Panesh (art)\r\n- Aleksey Gurevich (testing)\r\n\r\n\r\nLicense\r\n-------\r\nThe program is distributed under BSD license","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}