Northwestern Atlantic ocean microbial community difference in small and large size fractions characterised through amplicon sequence
We determined the difference in community diversity between two size fractions of water samples from a single site, and the possbility of merging two size fractions to a comparable unit to samples that were not size fractionated.
The data is publically available in NCBI under project accession number PRJNA785606 and the SraTableRun.csv.
Run generate_data.sh from the cloned repo from the bash_scripts folder. This file include all the code used to process the raw FASTQ files. Then, open the bb2_sf_microbial.ipynb jupyter notebook to generate the figures and statistics which depend on bb2022_functions.py. The R code was used to generate the PCoA plots, and the PERMANOVA analyses.
Resulting files are saved in the outputs folder.