Symbiosis Evolution lab - example amplicon data analysis pipeline using mothur

This repository contains a set of fairly detailed instructions for the analysis of custom amplicon data, such as those produced during the lab's first sequencing lane [link will be provided].

The pipeline is based on mothur v. 1.43, installed on the Institute of Environmental Sciences computing cluster. It also uses standard Unix shell commands, trim_galore (a versatile read trimmer), and refers to CodonCode Aligner, interactive software for working with sequence data.

Important links:

• mothur - Standard Operating Procedure for MiSeq amplicon data: https://www.mothur.org/wiki/MiSeq_SOP
• trim_galore: https://github.com/FelixKrueger/TrimGalore
• CodonCode Aligner: https://www.codoncode.com/aligner/

References:

• Schloss PD, et al. (2013): Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75(23):7537-41.
• Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology 79(17):5112-20.
• Schloss PD. (2019): Reintroducing mothur: 10 years later. Applied and Environmental Microbiology DOI:10.1128/AEM.02343-19