Coalescence project

Script used in the coalescence project:

When the river meets the sea: bacterial community dynamics after coalescence. Xiu Jia, Torsten Schubert, Rick Beeloo, Aristeidis Litos, Swapnil Doijad, Pim van Helvoort, Theodor Sperlea, Matthias Labrenz, and Bas E. Dutilh

Pipeline to analyze raw reads of full length 16S RNA gene

The 16S amplicon library was sequenced by Nanopore FLO-MIN114 flowcell with SQK-LSK114 kit. Please click here for scripts regarding raw reads processing.

• Basecalling
• Demultiplexing
• Taxonomic assignment

Downstream community analysis

Table cleaning

For table cleanning, check this script feature_table_clean_MPA_family_genus.Rmd, which includes

• Filter-out non bacteria reads.
• Removing taxa with a total reads less than 3 and that occur in fewer than 3 samples.
• Save table at family and genus level.
• CLR transformation.
• Combine "feature/OTU" table, taxonomy table, and metadata as phyloseq objects.

Tip

To view intermediate data and outputs generated at each step of the analysis, please refer to the accompanying HTML files produced with R Markdown (download and open by your browser, e.g. Chrome).

Rarefaction curves

To check the sequencing depth, I generated rarefaction curves by vegan pacakge in R, see script rarefaction_family_genus.Rmd

Diversity analysis

To analyse the community diveristy changes after coalescence, see script rarefaction_family_genus.Rmd