A bioinformatics primer for the analysis of illumina MiSeq data of litter-associated fungi and bacteria

Abstract

Metabarcoding of fungi and bacteria is rapidly evolving as a popular tool to assess the composition of microbial communities associated with decomposing plant litter. This development is generating vast volumes of raw data by high-throughput sequencing. One challenge in metabarcoding is to ensure the expertise to use the bioinformatics pipeline efficiently to examine the generated data. This chapter describes a flexible pipeline to analyze raw Illumina MiSeq sequences of litter-associated fungi and bacteria. The pipeline starts with the trimming of low-quality data, continues with clustering the retained sequences into taxonomic units, and is completed by taxonomic classification. The pipeline uses a set of commands on UNIX, whose implementation only requires basic computer knowledge. The chapter also includes scripts that users can adapt to their personal needs. All procedures are straightforward, so that MiSeq data can be analyzed on personal computers and even in classroom settings.