02_Input_file_BIOCOM-PIPE

BIOCOM-PIPE is a flexible and standalone suite of tools for processing data from high-throughput sequencing technologies (e.g. Roche 454 and Illumina), with a focus on the diversity of archaeal, bacterial, fungal, and photosynthetic microeukaryotic amplicons (targeting 16S, 18S and 23S rRNA genes). It includes several original methods: 1. Chimera removal based on read abundance and taxonomy, 2. Structure-based alignment of RNA homologs using covariance models (with the **Infernal** tool), 3. A post-clustering tool (called ReClustOR) to improve OTU consistency using a reference database. To launch this pipeline efficiently, and generate files for functional inference, any user can launch the BIOCOM-PIPE with the Input.txt file containing needed steps and associated parameters.