microbiomeutil 20101212+dfsg1-1build1 source package in Ubuntu
Changelog
microbiomeutil (20101212+dfsg1-1build1) bionic; urgency=high * No change rebuild to pick up -fPIE compiler default -- Balint Reczey <email address hidden> Tue, 03 Apr 2018 12:34:45 +0000
Upload details
- Uploaded by:
- Balint Reczey
- Uploaded to:
- Bionic
- Original maintainer:
- Ubuntu Developers
- Architectures:
- any all
- Section:
- misc
- Urgency:
- Very Urgent
See full publishing history Publishing
Series | Published | Component | Section | |
---|---|---|---|---|
Bionic | release | universe | misc |
Downloads
File | Size | SHA-256 Checksum |
---|---|---|
microbiomeutil_20101212+dfsg1.orig.tar.xz | 1.5 MiB | f6e75eb1ccbaca07c862f5e548850bb87c37279678250cd36f5804d673bbd56c |
microbiomeutil_20101212+dfsg1-1build1.debian.tar.xz | 9.7 KiB | 5d590505e604abd47fd0f67feb3c23709e9b521abbbf564e94e9d9604fa2f03e |
microbiomeutil_20101212+dfsg1-1build1.dsc | 2.5 KiB | e86c5ec92b1d65aa4325d99ea441e6fdce38d96ad8e59c8a7f211936c70ff33e |
Available diffs
Binary packages built by this source
- chimeraslayer: 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.
- microbiomeutil: 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.
- microbiomeutil-data: 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.
- nast-ier: 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.
- nast-ier-dbgsym: debug symbols for nast-ier
- wigeon: No summary available for wigeon in ubuntu cosmic.
No description available for wigeon in ubuntu cosmic.