7. Microbiome Informatics

Microbiome Informatics

Rebecca Ansorge, Falk Hildebrand, Andrea Telatin

Here we describe the bioinformatics and statistical procedures needed to analyse the output of sequencing experiments in microbiome studies, specifically: amplicon sequencing of 16S and ITS markers and whole metagenome shotgun (WMS) sequencing of faecal (stool) samples, starting from the raw output produced by Illumina sequencing (MiSeq 2×300 bp or longer for amplicons, and NextSeq/NovaSeq 2×150 bp or longer for whole metagenome shotgun). WMS data can be analysed with read-by-read classifiers or via a de novo assembly workflow that will allow you to recover metagenome associated genomes (MAGs).

7. Microbiome Informatics v1.0 [pdf]

Quadram Institute Best Practice in Microbiome Research: Microbiome Informatics v1.0 by Rebecca Ansorge, Falk Hildebrand, Andrea Telatin is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.