mnoguera / masterdadesomiques Goto Github PK

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DataSet for practical drylab work on 16s metagenomics data RawData: contains Quality controlled 10k illumina fastq https://drive.google.com/file/d/13OdeTDwXCGjLfivG4ZWpPb_R4D8kiF3z/view?usp=sharing Config: Contains metadata for further analysis

We will use SilvaDB to classify our sequence dataset SilvaDB is the most complete database of rRNA sequences and provides reduced and extended alignments for analysis Check it out at: http://www.arb-silva.de

For the practical session we will use these reference datasets formatted for DADA2 These datasets are quite large and may take quite a long time to download depending on your internet connection speed.

Please download all DB from https://drive.google.com/file/d/1Js4IVVsgZr6N6UEkm8xW23RNL5tXbGXs/view?usp=sharing And decompress into Training Subdir

We will use RDP algorithm by Wang et al (2012) for sequence classification as implemented in DADA2 Find the publication here http://aem.asm.org/content/73/16/5261

Drylab work will use DADA2 https://benjjneb.github.io/dada2/

Please install within your Rstudio environment:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("dada2", version = "3.10")

Additional R-packages: phyloseq, shortRead, digest