What I do

Since August 2023 I am working at the Food Systems Biotechnology group as a software engineer. My work in this group consist of developing and integrating bioinfomratics tools for metagenome-analysis with Qiime2.

Qiime2 is potent microbiome analysis tool that prioritizes transparency and reproducibility. It does so by featuring automated data tracking, a semantic type system, and a plugin system for expanded functionality.

My responsibilities in the devolving team include:

🔧 adding new functionalities to already existing plugins
👀 reviewing issues and PRs

For example I recently added BUSCO to the q2-moshpit plugin (Manni, 2021). BUSCO is a tool to quantify the quality of assembled metagenomes based on the presence of universal single-copy orthologues. The goal was to build a wrapper for the existing tool to make it available within Qiime2. Furthermore we sought to present the results through costume interactive visualizations like this one.

Example output from BUSCO analysis (image original from BUSCO's User Web-page).

Want to learn more?

🚀 Check out the Food Systems Biotechnology GitHub organization.

References

2021

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mosè Manni, Matthew R Berkeley, Mathieu Seppey, and 2 more authors

Molecular Biology and Evolution, Jul 2021

Abs

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly procedures and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here, we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying data sets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate BUSCO data set for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.