Coral 16S reanalysis

Introduction

This repository aims at reanalysing available 16S data from coral reefs and their surrounding environment.

In particular we are interested in papers who claim to investigate the core microbiome of various coral reef species.

Data

The data from the following papers will hopefully be used

Paper (doi)	Accession	N samples	metadata
10.1038/ismej.2015.39	PRJNA233450	71*	#6
10.1128/mBio.00560-16	PRJNA328211	1**	❎ (#2)
10.3390/microorganisms4030023	PRJNA313050	26	✅
10.3389/fmicb.2016.00458	PRJNA296835	23	✅
10.1038/srep27277	PRJNA312472	28	✅
10.1111/1758-2229.12412	PRJNA295144	2**	❎ (#3)
10.1128/AEM.00695-13	PRJNA189184	5	✅
10.1038/ismej.2016.9	PRJNA310360	120***	✅
10.1111/mec.13251	PRJNA277291	54	✅
10.3354/meps10197	SRP010998	12	✅
10.1111/mec.13567	PRJNA282461	41	❎ #5
10.1038/srep07320	SRR1263017	2**	❎ (#4)
10.1038/srep45362	PRJNA352338	55	✅
10.1371/journal.pone.0067745	PRJNA192455	10	✅
10.1111/1462-2920.13840	PRJNA302254	3	❎ #7
10.7717/peerj.2529	PRJNA297333	5	✅
10.1007/s00248-016-0858-x	PRJNA312774	60	✅
10.1371/journal.pone.0100316	PRJNA231864	34	✅
10.1371/journal.pone.0076095	PRJNA193567	16	✅

* no data available in the bioprojects yet, has been the object of an enquiry.
** Data without sufficient metadata / with pooled samples will not be analysed.
*** The samples that were disturbed with antibiotics will not be considered for reanalysis.

See data/samples.txt for more information

Don't see your dataset / article in the list? Open an issue and I'll be more than happy to use it!

Setup

To run the code, you'll need nextflow and docker installed.

Download the data

nextflow run download.nf

which will download the data into the data directory,

The data consists of compressed fastq files and is approximately 2 Gb. You'll need 4Gb of storage for downloading (due the the nextflow temp files that we keep in case we want to resume an interrupted download)

You can remove the temporary files with

make clean

Download the SILVA database

The following command will download the necessary files to use the SILVA database with dada2

make db

This will create a db directory

Run the pipeline

WORK IN PROGRESS

Data QC and Adapter trimming

nextflow run qc.nf
gzip data/trimmed/*.fastq

You'll need the same storage space as for downloading the data. Once again you can cleanup the temporary with make clean

Run DADA2

nextflow run dada.nf

Data visualisation

wip

see analysis.Rmd