Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.
|Author||Anja Lange [aut, cre], Daniel Hoffmann [aut]|
|Date of publication||2016-01-19 13:09:23|
|Maintainer||Anja Lange <email@example.com>|
|License||GPL (>= 3)|
accepted.amplicons: List Of Amplicon Indices That Passed Filter Criteria
ampliconduo: Apply Fisher's Exact Tests To Two Amplicon Frequency Sets Of...
AmpliconDuo-package: Statistical Analysis Of Amplicon Data Of The Same Sample To...
ampliconfreqs: SSU Amplicon Frequencies Of Different Sampling Sites (Short...
ampliconfreqs.long: SSU Amplicon Frequencies Of Different Sampling Sites
amplicons: Example List of Ampliconduo Data Frames
discordance.delta: Measure Of Discordance Between Two Amplicon Data Sets
filter.ampliconduo: AmpliconDuo Amplicon Filter
filter.ampliconduo.set: AmpliconDuo List Amplicon Filter
plotAmpliconduo: Frequency-Frequency Plot Focusing On Significant Deviations...
plotAmpliconduo.set: Frequency-Frequency Plot Arrangement Focusing On Significant...
plotORdensity: Probability Density Plot Of Odds Ratios
site.f: Sampling Site Short Names