{"name":"Sniffles","description":"An algorithm for structural variation detection from third generation sequencing alignment.","homepage":"https://github.com/fritzsedlazeck/Sniffles","biotoolsID":"sniffles","biotoolsCURIE":"biotools:sniffles","version":[],"otherID":[{"value":"RRID:SCR_017619","type":"rrid","version":null}],"relation":[],"function":[{"operation":[{"uri":"http://edamontology.org/operation_2403","term":"Sequence analysis"},{"uri":"http://edamontology.org/operation_3228","term":"Structural variation detection"}],"input":[{"data":{"uri":"http://edamontology.org/data_1383","term":"Sequence alignment (nucleic acid)"},"format":[{"uri":"http://edamontology.org/format_2572","term":"BAM"}]}],"output":[{"data":{"uri":"http://edamontology.org/data_3498","term":"Sequence variations"},"format":[{"uri":"http://edamontology.org/format_3016","term":"VCF"}]}],"note":null,"cmd":null}],"toolType":["Command-line tool"],"topic":[{"uri":"http://edamontology.org/topic_3175","term":"DNA structural variation"},{"uri":"http://edamontology.org/topic_3168","term":"Sequencing"}],"operatingSystem":["Linux","Windows","Mac"],"language":[],"license":"MIT","collectionID":[],"maturity":"Mature","cost":"Free of charge","accessibility":"Open access","elixirPlatform":[],"elixirNode":[],"elixirCommunity":[],"link":[],"download":[{"url":"https://github.com/fritzsedlazeck/Sniffles","type":"Software package","note":"A Github page with source code, documentation and test datasets.","version":null}],"documentation":[{"url":"https://github.com/fritzsedlazeck/Sniffles/wiki","type":["General"],"note":"A Github wiki."}],"publication":[{"doi":"10.1038/s41592-018-0001-7","pmid":"29713083","pmcid":"PMC5990442","type":[],"version":null,"note":null,"metadata":{"title":"Accurate detection of complex structural variations using single-molecule sequencing","abstract":"Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings.","date":"2018-06-01T00:00:00Z","citationCount":902,"authors":[{"name":"Sedlazeck F.J."},{"name":"Rescheneder P."},{"name":"Smolka M."},{"name":"Fang H."},{"name":"Nattestad M."},{"name":"Von Haeseler A."},{"name":"Schatz M.C."}],"journal":"Nature Methods"}}],"credit":[{"name":"Fritz J Sedlazeck","email":"fritz.sedlazeck@gmail.com","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":["Primary contact"],"note":null}],"owner":"ELIXIR-EE","additionDate":"2018-05-15T15:47:56Z","lastUpdate":"2024-11-24T20:24:19.795436Z","editPermission":{"type":"private","authors":[]},"validated":1,"homepage_status":0,"elixir_badge":0,"confidence_flag":null}