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update READme methods
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# Island Sampling Day (ISD)

The Island Sampling Day draws inspiration from the Ocean
Sampling Day that is a consortium that facilitates yearly samplings
in stations from all around the world. This has great applications
in monitoring and comprehending the
complexity of the ocean microbiome and it's drivers.

The Island Sampling Day has been organised in two islands, Moorea
in the French Polynisia and Crete in Greece.

## Soil microbiome sampling

The metagenomic revolution enabled environmental microbial biodiversity
studies which for the past 20 years, have sampled multiple local and
large scale regions (e.g. France microbiome, Earth Microbiome). These
studies indicated that microbes are omnipresent and impact global ecosystem
processes through their abundance, versatility and biotic interactions
(i.e. interactomes). Additionally, microbes influence the major nutrient
cycles and ecosystem functions, such as plant and animal productivity.
Changes in the structure of microbial communities can be indicative of
ecosystem tipping points e.g aridification.

## Chapter one: Crete

ISD is a soil microbiome study to explore environmental drivers of community
composition across ecosystems in the island of Crete, Greece.

A snapshot of the prokaryotic diversity across the island of Crete. Aim to:

1. Put metadata into action through a citizen science project
2. describe the first full island microbial community assessment
3. shed light on phylotypes found not to be all the same across Crete’s distinct terrestrial habitats (<i>intra comparison</i>)
4. present a “local” (island) vs “global” (world, e.g. EMP) soil phylotype comparative analysis (<i>inter comparison</i>)
1. Put metadata into action through a citizen science project to demonstrate their value in future samplings
2. Describe the first full island microbial community assessment
3. Shed light on phylotypes found not to be all the same across Crete’s distinct terrestrial habitats (<i>intra comparison</i>)
4. Present a “local” (island) vs “global” (world, e.g. EMP) soil phylotype comparative analysis (<i>inter comparison</i>)

This repository holds ISD molecular ecology analysis pertinent scripts.
ISD sequence data are available as a <a href="https://www.ebi.ac.uk/ena/data/view/PRJEB21776" target="blank">European Nucleotide Archive repository project</a>.

## Contents

* [Sampling](#sampling)
* [Methods](#methods)
* [Sampling](#sampling)
* [Scripts](#scripts)
* [Data retrieval](#data-retrieval)
* [Data integration](#data-integration)
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* [Citation](#citation)
* [Licence](#licence)

## Methods

* Sampling
* MTA and soil permits
* DNA extraction and amplification
* Sequencing
* Soil physical chemistry
* Bioinformatics and Ecological analysis

## Sampling

During the 18th of Genome Standards Consortium workshop the participants along
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