Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities
This repository incorporates the analysis pipelines applied to 16S amplicon and PacBio HiFi read metagenomes in the study "Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities".
There are four distinct sections to the analysis, each encapsulated on a different wiki page within this repository. The sections include:
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16S Amplicon analysis : raw sequence data processing, DADA2 pipeline, statistical analysis and visualisation in RStudio. Amplicon Sequence Variant abundance tables, metadata and R script to recreate statistical analysis and plots are provided.
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Network analysis : R based network analysis applied to Amplicon Sequence Variant dynamics over the two, two-year time series. Necessary input files and R script to reproduce are provided.
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Metagenome assembled genome recovery : detailed description of pipeline used to recover metagenome-assembled genomes, including the lines of code used to run the employed tools.
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Metagenomic long-read taxonomic and functional profiling : detailed description along with code used to functionally and taxonomically annotate metagenomic HiFi reads.