chimeraslayer
detects likely chimeras in PCR amplified DNA
Command lineScience
Not tested on a device yet. What that means
Commands in the package
chimeraslayer
About chimeraslayer
From Debian's package description
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.
From Debian's description of the chimeraslayer package, under that package's license.
Dependencies
Depends on
microbiomeutil-datacdbfastancbi-blast+-legacy
Recommends
Related apps
- microbiomeutilMicrobiome Analysis UtilitiesCommand line
- wigeonreimplementation of the Pintail 16S DNA anomaly detection utilityCommand line
- nast-ierNAST-based DNA alignment toolCommand line
- mipeTools to store PCR-derived dataCommand line
- ecopcrestimate PCR barcode primers qualityCommand line
- ncbi-epcrTool to test a DNA sequence for the presence of sequence tagged sitesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the chimeraslayer package, under that package's license.
- Description: Debian's description of the chimeraslayer package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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