PEMA v.2.1.4 is now released!

04 Dec 2021

A new version of PEMA is just released!

This new PEMA release:

• is based on a new pemabase Docker image (pemabase:v.2.1.1) which is now completely indepedent from any local resources and the user can build it through the Dockerfile.pemabase file
• a new marker gene, the 12S rRNA, is now also supported, by exploiting the 12S Vertebrate Classifier v2.0.0-ref database
• for the case of 18S rRNA marker gene, the PR2 database has been integrated so now the user may select between Silva and PR2
• thanks to the ncbi-taxonomist software, PEMA now provides an extended OTU/ASV table where in last column the NCBI Taxonomy Id for the taxonomic level closer to the species name rank for which there is one, is available

In addition, in this release:

• a sannity_check folder with datasets and parameters files for multiple combinations are now available, so tests can be performed to check whether pema runs properly after edits.
• bugs during the analysis of 18S data have been fixed
• the perSample outputs have been fixed
• convertion of non ena format raw data for multiple sequencers is supported

You may find pema v.2.1.4 as a Docker image or as a Singularity.

Many thanks to Christina Pavloudi for all her feedback and insight!

This release was to address some of the challenges set by the ARMS-MBON project of ASSEMBPLE Plus.

More features are about to be integrated in the future, for example what about pseudogenes and NUMTS ??

You can always share your thoughts on metabarcoding issues and challenged throught PEMA’s Discussions!