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Source: microbiomeutil
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>,
Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
cdbfasta,
blast2
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/microbiomeutil
Vcs-Git: https://salsa.debian.org/med-team/microbiomeutil.git
Homepage: http://microbiomeutil.sourceforge.net/
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,
blast2
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
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.
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