Tutorial scripts and data for Claident.
- メタバーコーディング法概説：夢の技術の夢のない現実の話 (Introduction to metabarcoding: The reality of dream technology) Speech in Japanese with English slides
- ClaidentとRによる環境DNAメタバーコーディング分析講座：塩基配列データ処理から生態学的分析まで (Lecture course on environmental DNA metabarcoding using Claident and R: From nucleotide sequence data processing to ecological analyses) Speech in Japanese with English slides and auto-translated English subtitles
- ClaidentとRによる環境DNA「定量」メタバーコーディング分析講座：塩基配列データ処理から生態学的分析まで (Lecture course on "quantitative" environmental DNA metabarcoding using Claident and R: From nucleotide sequence data processing to ecological analyses) Speech in Japanese with English slides
Claident, associated databases and programs need to be installed. Use ClaidentInstaller to install them. In addition, this package need to be downloaded and extracted to working directory. For wordcloud image generation ("clplotwordcloud" command), Google Chrome or Chromium is also required.
R and several packages need to be installed. Install R, and then, execute the following command in R
library(parallel)
install.packages(c("vegan", "colorspace", "RColorBrewer", "tidyverse", "ggsci", "khroma", "picante", "bipartite", "geosphere", "foreach", "doParallel", "mpmcorrelogram", "pvclust"), repos="http://cloud.r-project.org/", clean=T, upgrade="never", Ncpus=detectCores())
You might need to install several programs and/or libraries such as libssl or libgdal before executing the above package installation in R. If you are trying to run this tutorial on Ubuntu or Debian, the following command may helps you.
sudo apt install libssl-dev libgdal-dev
Just download this package and extract to working directory.
See the following shell scripts, inputs and outputs.
- runClaident_singleend_woSTD.sh
- runClaident_overlappedpairedend_woSTD.sh
- runClaident_nonoverlappedpairedend_woSTD.sh
- runClaident_overlappedpairedend_wSTD.sh
See the following R codes, inputs and outputs.