Package: rchime 0.1.3

Pat Schloss

rchime: Detect and Remove Chimeras from Amplicon Sequence Analysis Data

Detect and remove chimeras from your amplicon sequence analysis using reference-based or de novo approaches. The 'rchime' package implements the 'VSEARCH' algorithms described in Rognes et al. (2016) <doi:10.7717/peerj.2584>. 'VSEARCH' builds on the work of Edgar,R.C. et al. (2011) <doi:10.1093/bioinformatics/btr381>.

Authors:Sarah Westcott [aut], Pat Schloss [cph, cre], Torbjorn Rognes [cph], Frederic Mahe [cph], Tomas Flouri [cph], Christopher Quince [cph], Ben Nichols [cph]

rchime_0.1.3.tar.gz
rchime_0.1.3.zip(r-4.7-x86_64)rchime_0.1.3.zip(r-4.7-arm64)rchime_0.1.3.zip(r-4.6-x86_64)rchime_0.1.3.zip(r-4.6-arm64)rchime_0.1.3.zip(r-4.5-x86_64)
rchime_0.1.3.tgz(r-4.6-x86_64)rchime_0.1.3.tgz(r-4.6-arm64)rchime_0.1.3.tgz(r-4.5-x86_64)rchime_0.1.3.tgz(r-4.5-arm64)
rchime_0.1.3.tar.gz(r-4.7-arm64)rchime_0.1.3.tar.gz(r-4.7-x86_64)rchime_0.1.3.tar.gz(r-4.6-arm64)rchime_0.1.3.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rchime/json (API)

# Install 'rchime' in R:
install.packages('rchime', repos = c('https://mothur.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mothur/rchime/issues

Pkgdown/docs site:https://mothur.org

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

amplicon-sequencingchimeracpp

5.48 score 5 scripts 226 downloads 5 exports 91 dependencies

Last updated from:799f0db2b9. Checks:14 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK226
linux-devel-x86_64OK241
source / vignettesOK350
linux-release-arm64OK239
linux-release-x86_64OK264
macos-release-arm64OK182
macos-release-x86_64OK369
macos-oldrel-arm64OK214
macos-oldrel-x86_64OK394
windows-devel-arm64OK330
windows-devel-x86_64OK299
windows-release-arm64OK428
windows-release-x86_64OK243
windows-oldrel-x86_64OK234
wasm-releaseFAIL127

Exports:rchimerchime_examplerchime_optionssilva_goldstrollur_multi_sample_small

Dependencies:apebeeswarmbitbit64cellrangerclicliprclustercommonmarkcpp11crayoncurldata.tablediffobjdigestdplyrecodiveemmeansestimabilityfarverfillpatterngenericsggbeeswarmggnewscaleggplot2ggrepelggtextgluegridtextgtablehmsisobandjpegjsonlitelabelinglatticelifecyclelitedownmagrittrmarkdownMASSMatrixmgcvmicroseqmvtnormnlmenumDerivparallellypatchworkpermutepillarpkgconfigplyrpngprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rbiomRcerealRColorBrewerRcppRcppThreadRcppXsimdreadrreadxlrematchrlangS7scalesstringistringrstrollurtibbletidyrtidyselecttzdbutf8vctrsveganviporviridisLitevroomwaldowithrxfunxml2yaml

chimera_report
Overview | Example
Rendered fromchimera_report.Rmdusingknitr::rmarkdown

Last update: 2026-07-28
Started: 2026-03-24

De novo Chimera Detection
Overview | Creating strollur objects | Loading data.frames | Removing chimeras | Results
Rendered fromdenovo_based_detection.Rmdusingknitr::rmarkdown

Last update: 2026-07-28
Started: 2026-03-24

Reference Based Chimera Detection
Overview | Creating strollur objects | Loading data.frames | Removing chimeras | Results
Rendered fromreference_based_detection.Rmdusingknitr::rmarkdown

Last update: 2026-07-28
Started: 2026-03-24

Getting Started
Installing rchime | Tutorials to help you get started
Rendered fromrchime.Rmdusingknitr::rmarkdown

Last update: 2026-07-07
Started: 2025-04-23