{"refrec":{"BRefID":331941,"RR":"<b>Abdala Asbun, A.; Besseling, M.A.; Balzano, S.; van Bleijswijk, J.D.L.; Witte, H.J.; Villanueva, L.; Engelmann, J.C.</b> (2020). <i>Cascabel</i>: A scalable and versatile amplicon sequence data analysis pipeline delivering reproducible and documented results. <i>Frontiers in Genetics 11</i>: 489357. <a href=\"https://doi.org/10.3389/fgene.2020.489357\" target=\"_blank\">https://doi.org/10.3389/fgene.2020.489357</a>","BEntID":325553,"PublicFlag":1,"CheckedFlag":0,"wosflag":1,"vabbflag":0,"RefStringPartII":". <i>Frontiers in Genetics 11</i>: 489357. <a href=\"https://doi.org/10.3389/fgene.2020.489357\" target=\"_blank\">https://doi.org/10.3389/fgene.2020.489357</a>","DocTypID":8,"DocType":"Journal article","MarineFlag":0,"FreshFlag":0,"BrackishFlag":0,"TerrestrialFlag":0,"Authorstring":"Abdala Asbun, A.; Besseling, M.A.; Balzano, S.; van Bleijswijk, J.D.L.; Witte, H.J.; Villanueva, L.; Engelmann, J.C.","OrigTitleTranslFlag":0,"Authorstringtrunc":"Abdala Asbun, A. <i>et al.</i>","Englishabstract":"  Marker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c    oxidase I (CO1) is a popular means to assess microbial communities of the    environment, microbiomes associated with plants and animals, as well as    communities of multicellular organisms <em>via</em> environmental DNA    sequencing. Since this technique is based on sequencing a single gene, or    even only parts of a single gene rather than the entire genome, the number    of reads needed per sample to assess the microbial community structure is    lower than that required for metagenome sequencing. This makes marker gene    sequencing affordable to nearly any laboratory. Despite the relative ease    and cost-efficiency of data generation, analyzing the resulting sequence    data requires computational skills that may go beyond the standardrepertoire of a current molecular biologist/ecologist. We have developed    <em>Cascabel</em>, a scalable, flexible, and easy-to-use amplicon sequence    data analysis pipeline, which uses Snakemake and a combination of existingand newly developed solutions for its computational steps.    <em>Cascabel</em> takes the raw data as input and delivers a table of    operational taxonomic units (OTUs) or Amplicon Sequence Variants (ASVs) in    BIOM and text format and representative sequences. <em>Cascabel</em> is a    highly versatile software that allows users to customize several steps of    the pipeline, such as selecting from a set of OTU clustering methods or    performing ASV analysis. In addition, we designed <em>Cascabel</em> to run    in any linux/unix computing environment from desktop computers to computing    servers making use of parallel processing if possible. The analyses and    results are fully reproducible and documented in an HTML and optional pdf    report.","AbstractOtherLang":null,"BibLvlCode":"AS","StandardTitle":"<i>Cascabel</i>: A scalable and versatile amplicon sequence data analysis pipeline delivering reproducible and documented results","OrigTitleLangCode":"en","OrigTitleLangCodeExtended":"eng","OrigTitleLangID":15,"DateLastModified":{"date":"2024-12-10 01:33:01.897972","timezone_type":1,"timezone":"+01:00"},"UserAccessRight":null,"UserAccID":null,"AuthorKeywords":null,"OtherDescriptors":null,"Notes":null,"AnaPub":2020,"MonPub":null,"DateUpdate":"2020-12-14","DateCreate":"2020-12-14","SecASFANote":null,"ConfID":null,"PeerRev":1,"VlizCoreFlag":1,"WoScode":"WOS:000595399800001","VABBcode":null,"OpenAcc":1,"DOI":"10.3389/fgene.2020.489357"},"refs":null,"anarec":{"AnaID":331941,"PubliDate":2020,"Pagination":"489357","XtraPublOfAnaID":null,"ISBN":null,"Volume":"11","Issue":null,"BRefMon":null,"BRefMonRR":null,"BRefXtra":null,"BRefXtraRR":null,"SerBRefID":268435,"SerRR":"Frontiers in Genetics. 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