J. Saraiva

The paper introduces an automated pipeline for whole-genome sequencing analysis of microbial pesticides to improve hazard characterization and risk assessment.

PHI is a Galaxy-based workflow that automates prophage-host interaction analysis and generates standardized reports, detecting 41 prophages across 14 hosts in a mock community.

HVRLocator identifies hypervariable regions in 16S rRNA datasets to improve metadata quality and enable accurate large-scale microbiome analysis.

The paper simulates microbial communities to show sequencing depth and false positives significantly affect metagenome-assembled genome recovery accuracy.

MuDoGeR simplifies genome recovery from metagenomes for non-experts, demonstrating effectiveness across various sample sizes.

The paper recovers 447 eukaryotic bins from metagenomes, highlighting challenges in genome reconstruction and the need for improved methods and reference genomes.

OrtSuite predicts microbial interactions based on genomic content for specific ecosystem processes using ortholog clustering and user-defined functions.

PredicTF predicts bacterial transcription factors in microbial communities using genomic and metagenomic data from environmental isolates and anammox bioreactors.

TerrestrialMetagenomeDB curates and standardizes metadata for terrestrial metagenomes to facilitate comparison and meta-analysis across datasets.