Source: microbiomeutil Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Section: science Priority: optional Build-Depends: debhelper-compat (= 13), cdbfasta, ncbi-blast+-legacy Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/microbiomeutil Vcs-Git: https://salsa.debian.org/med-team/microbiomeutil.git Homepage: http://microbiomeutil.sourceforge.net/ Rules-Requires-Root: no Package: microbiomeutil Architecture: all Depends: ${misc:Depends}, chimeraslayer, nast-ier, wigeon Description: Microbiome Analysis Utilities The microbiomeutil package comes with the following utilities: * ChimeraSlayer: ChimeraSlayer for chimera detection. * NAST-iEr: NAST-based alignment tool. * WigeoN: A reimplementation of the Pintail 16S anomaly detection utility * RESOURCES: Reference 16S sequences and NAST-alignments that the tools above leverage. Package: chimeraslayer Architecture: all Depends: ${misc:Depends}, microbiomeutil-data, cdbfasta, ncbi-blast+-legacy Recommends: nast-ier Description: detects likely chimeras in PCR amplified DNA ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500bp). . Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences: . 1. the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera 2. candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence 3. the NAST alignment of the query sequence is improved in a ‘chimera-aware’ profile-based NAST realignment to the selected reference parent sequences 4. an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences. . To run Chimera Slayer, you need NAST-formatted sequences generated by the nast-ier utility. . ChimeraSlayer is part of the microbiomeutil suite. Package: nast-ier Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends}, microbiomeutil-data, cdbfasta Recommends: ncbi-blast+ Description: NAST-based DNA alignment tool The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences. . The alignment algorithm involves global dynamic programming profile alignment to fixed (NAST-formatted) multiply aligned template sequences without any end-gap penalty. . NAST-iEr is part of the microbiomeutil suite. Package: wigeon Architecture: all Depends: ${misc:Depends}, microbiomeutil-data Recommends: nast-ier Description: reimplementation of the Pintail 16S DNA anomaly detection utility WigeoN examines the sequence conservation between a query and a trusted reference sequence, both in NAST alignment format. Based on the sequence identity between the query and the reference sequence, there is an expected amount of variation among the alignment. If the observed variation is greater than the 95% quantile of the distribution of variation observed between non-anomalous sequences, then it is flagged as an anomaly. . WigeoN is a flexible command-line based reimplementation of the Pintail algorithm Appl Environ Microbiol. 2005 Dec;7112:7724-36. . WigeoN is useful for flagging chimeras and anomalies only in near full-length 16S rRNA sequences. WigeoN lacks sensitivity with sequences less than 1000 bp. . To run WigeoN, you need NAST-formatted sequences generated by the nast-ier utility. . WigeoN is part of the microbiomeutil suite. Package: microbiomeutil-data Architecture: all Depends: ${misc:Depends} Enhances: chimeraslayer, nast-ier, wigeon Description: Reference 16S sequences and NAST-alignments used by microbiomeutil tools Reference data for tools in the microbiomeutil package. The algorithms used by the tools chimeraslayer, nast-ier and wigeon are based on reference data which are provided by this package.