The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data

The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/and amplicon sequence variants (ASVs) retrieved from such studies do not get a taxonomic assignment with a reference sequence. To assess and investigate such sequences, we have developed the Dark mAtteR iNvestigator (DARN) software tool. For this purpose, a reference COI-oriented phylogenetic tree was built from 1,593 consensus sequences covering all the three domains of life. DARN makes use of this phylogenetic tree to investigate COI pre-processed sequences of amplicon samples to provide both a tabular and a graphical overview of their phylogenetic assignments.

We demonstrate that a large proportion of non-target prokaryotic organisms, such as bacteria and archaea, are also amplified in eDNA samples and we suggest prokaryotic COI sequences to be included in the reference databases used for the taxonomy assignment to allow for further analyses of dark matter

Read more for the darn software

fluxomics training school 2021 - Elixir Metabolomics Community

fluxomics training school 2021 - Elixir Metabolomics Community

Joining the Fluxomics training school of Elixir Metabolomics Community has been probably the highlight of all online events during this COVID-19 period.

Beyond learning the basics of the various methods used when studying fluxes, I was so glad that I was proved wrong about online events and whether the attendees can actually interact one another.

A big, big “thank you” to all members of the organizing committee and a promise for an in-person meeting sometime soon! 🦠 🧬

Gsoc Completed

My Google Summer of Code project has been completed!

You may find here what @GeomScale and I did over the last 10 weeks!

You can also find our project among the GSoC 2021 projects.

We are still in the start, but GSoC many thanks for supporting our efforts for random sampling over the flux space of microbial communities metabolic networks!

A Revised Version Of Darn Now Available

A revised version of the darn software tool is now available. Dark mAtteR iNvestigator (DARN) uses a COI reference tree covering all domains of life (eukaryotes, bacteria, archaea) to assign your sequences to the 3 domains of life.

Its purpose is not to provide you with certain taxonomic assignment but to give an overview of the species present.

PFam oriented bacterial sequences have been added in the initial sequences dataset and allowing us to cover 371 families plus 60 taxonomic groups of higher level not assigned in family.

To get this latest version, you just need to install docker and run

docker pull hariszaf/darn:latest

Have fun discovering more and more bacteria on your COI amplicon data! :tada: 🥳

Imbbc Hpc Publication

Our manuscript on the history, the usage and the scnientific impact of the IMBBC HPC facility over the last 10 years was just published on the GigaScienece journal.

Have a look overe here.

history

0s and 1s in marine molecular research: a regional HPC perspective Open Access

High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.

Darn@biorxiv

The Dark mAtteR iNvestigator darn software tool for the identification of the unassigned sequences of COI data is on the road!

Here you may find the corresponding pre-print!

darn is available as a Docker image.

You may find more about how to install and how to use darn through its GitHub repository.

Pagination


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