| Name : R-debar
| |
| Version : 0.1.1
| Vendor : obs://build_opensuse_org/devel:languages:R
|
| Release : lp153.1.4
| Date : 2024-06-14 11:53:01
|
| Group : Development/Libraries/Other
| Source RPM : R-debar-0.1.1-lp153.1.4.src.rpm
|
| Size : 0.83 MB
| |
| Packager : (none)
| |
| Summary : A Post-Clustering Denoiser for COI-5P Barcode Data
|
Description :
The \'debar\' sequence processing pipeline is designed for denoising high
throughput sequencing data for the animal DNA barcode marker cytochrome
c oxidase I (COI). The package is designed to detect and correct
insertion and deletion errors within sequencer outputs. This is
accomplished through comparison of input sequences against a profile
hidden Markov model (PHMM) using the Viterbi algorithm (for algorithm
details see Durbin et al. 1998, ISBN: 9780521629713). Inserted base
pairs are removed and deleted base pairs are accounted for through the
introduction of a placeholder character. Since the PHMM is a
probabilistic representation of the COI barcode, corrections are not
always perfect. For this reason \'debar\' censors base pairs adjacent to
reported indel sites, turning them into placeholder characters (default
is 7 base pairs in either direction, this feature can be disabled).
Testing has shown that this censorship results in the correct sequence
length being restored, and erroneous base pairs being masked the vast
majority of the time (>95%).
|
RPM found in directory: /packages/linux-pbone/ftp5.gwdg.de/pub/opensuse/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Leap_15.3/x86_64 |
