Package: debar 1.0.1
debar: A Post-Clustering Denoiser for COI-5P Barcode Data
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%).
Authors:
debar_1.0.1.tar.gz
debar_1.0.1.zip(r-4.5)debar_1.0.1.zip(r-4.4)debar_1.0.1.zip(r-4.3)
debar_1.0.1.tgz(r-4.4-any)debar_1.0.1.tgz(r-4.3-any)
debar_1.0.1.tar.gz(r-4.5-noble)debar_1.0.1.tar.gz(r-4.4-noble)
debar_1.0.1.tgz(r-4.4-emscripten)debar_1.0.1.tgz(r-4.3-emscripten)
debar.pdf |debar.html✨
debar/json (API)
| # Install 'debar' in R: |
| install.packages('debar', repos = c('https://cnuge.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cnuge/debar/issues
bioinformaticsdenoisingdna-barcodingdna-sequencinghidden-markov-modelmachine-learning
Last updated 11 months agofrom:bbd56431ad. Checks:OK: 2 NOTE: 2 ERROR: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win | ERROR | Nov 08 2024 |
| R-4.5-linux | NOTE | Nov 08 2024 |
| R-4.4-win | ERROR | Nov 08 2024 |
| R-4.4-mac | NOTE | Nov 08 2024 |
| R-4.3-win | ERROR | Nov 08 2024 |
| R-4.3-mac | OK | Nov 08 2024 |
Exports:aa_checkaa_check.DNAseqadj_seqadjustadjust.DNAseqcensored_translationcol_modeconsensus_sequencedenoisedenoise_filedenoise_file.defaultdenoise_listdenoise.defaultdir_checkDNAseqex_nt_listexample_nt_stringexample_nt_string_errorsframeframe.DNAseqindividual_DNAbinins_front_trimleading_insmeta_checknew_DNAseqnt_coi_PHMMoutseqoutseq.DNAseqprint.DNAseqread_fastaread_fastqrev_compset_frametranslate_codontriple_delstriple_insvalidate_DNAseqwrite_fastawrite_fasta.DNAseqwrite_fastqwrite_fastq.DNAseqwrite_wrapperwrite_wrapper.DNAseq
Dependencies:ade4apeaphidaskpassdigestkmerlatticeMASSnlmeopensslphylogrampixmapRcppRcppArmadillosegmentedseqinrspsys
debar - details of the denoising algorithm
Rendered fromdebar-algorithm-details.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2021-08-31
Started: 2019-11-29
debar - DEnoising COI-5P BARcode data
Rendered fromdebar-vignette.Rmdusingknitr::rmarkdownon Nov 08 2024.Last update: 2020-06-16
Started: 2019-11-20
