Snakemake workflow for analyzing the 12S rRNA barcoding sequencing data

2023-05-15

This Snakemake pipeline is built for processing raw Illumina metabarcoding data, identifying species in the samples, and counting abundance. It will give abundance report per taxon level in excel and generate krona plot.

Dependencies:

• QIIME 2 release: 2023.2
• snakemake v. 7.25.3
• wget
• R version 4.1.2 (2021-11-01)
  • BiocManager (v. 1.30.20)
  • tidyverse (v. 2.0.0)
  • phyloseq (v. 1.38.0)
  • ggplot2 (v. 3.4.2)
  • psadd (v. 0.1.3))
  • qiime2R (v. 0.99.6)
  • xlsx (v. 0.6.5)
  • remotes (v. 2.4.2)
  • rmarkdown (v. 2.21)

My computer

## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=id_ID.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=id_ID.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=id_ID.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=id_ID.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] rmarkdown_2.21  lubridate_1.9.2 forcats_1.0.0   stringr_1.5.0  
##  [5] dplyr_1.1.2     purrr_1.0.1     readr_2.1.4     tidyr_1.3.0    
##  [9] tibble_3.2.1    ggplot2_3.4.2   tidyverse_2.0.0
## 
## loaded via a namespace (and not attached):
##  [1] pillar_1.9.0     compiler_4.1.2   tools_4.1.2      digest_0.6.31   
##  [5] timechange_0.2.0 evaluate_0.21    lifecycle_1.0.3  gtable_0.3.3    
##  [9] pkgconfig_2.0.3  rlang_1.1.1      cli_3.6.1        rstudioapi_0.14 
## [13] yaml_2.3.7       xfun_0.39        fastmap_1.1.1    withr_2.5.0     
## [17] knitr_1.42       generics_0.1.3   vctrs_0.6.2      hms_1.1.3       
## [21] grid_4.1.2       tidyselect_1.2.0 glue_1.6.2       R6_2.5.1        
## [25] fansi_1.0.4      tzdb_0.4.0       magrittr_2.0.3   scales_1.2.1    
## [29] htmltools_0.5.5  colorspace_2.1-0 utf8_1.2.3       stringi_1.7.12  
## [33] munsell_0.5.0