Meta16s

An all-in-one solution for streamlined 16s analyses.

Meta16s is an all-in-one pipeline for the analysis of 16s NGS data. Meta16s takes raw paired-end NGS reads (.fastq.gz) as an input in order to generate a cleaned taxonomic abundance file (biom and tsv).

Meta16s requires Python2, Conda and USEARCH in order to run. All other dependencies will be downloaded automatically. In addition, the GreenGenes and RDP databases are required to be setup within the Meta16s folder.

Quick Start:

• Clone the Meta16s repository
• Extract the USEARCH binary (usearch11.0.667_i86linux32) into the Meta16s folder
• Extract the GreenGenes database (gg_13_8_otus) into the databases folder
• Activate the Meta16s conda environment (Meta16s.yml)
• Download the RDP 11 database (current_Bacteria_unaligned.fa)
• Run SequenceMatch train to create the databases/rdp/ folder
• Copy read files into the "sequences" folder
• Make sure the paired-end reads are named "<unique_name>_R1.fastq.gz" and "<unique_name>_R2.fastq.gz" respectively
• Run Meta16s (Reference_Analyzer_16s.py)

Licence

This project is licensed under the GPLv3 Licence. See the LICENSE file for more details.