hariszaf/pema repository overview

P.E.M.A. is a pipeline for four marker genes, 16S rRNA (Microbes) , 18S rRNA and COI (Eukaryotes) and ITS (Fungi). As input, P.E.M.A. accepts fastq files as returned by Illumina sequencing platforms. P.E.M.A. processes the reads from each sample and returns an OTU-table with the taxonomies of the organisms found and their abundances in each sample. It also returns statistics and a FASTQC diagram about the quality of the reads for each sample. Finally, in the case of 16S, P.E.M.A. returns alpha and beta diversities, and make correlations between samples. The last step is facilitated by the phyloseq R package which allows the downstream 16S amplicon analysis of microbial profiles.

In the COI case, two clustering algorithms can be performed by P.E.M.A. (CROP and SWARM), while in the 16S, two approaches for taxonomy assignment are supported: alignment- and phylogenetic-based. For the latter, a reference tree with 1000 taxa was created using SILVA_132_SSURef, EPA-ng and RaxML-ng.

PEMA is also available as Singularity container; you may find it here⁠.

For more information about PEMA you may read its relative publication⁠ and for further instructions about how to use it, you may visit our github repository⁠