#28 · Tools & infrastructure
Automated pipelines convert raw sequence data into queryable, reusable genomic resources
The common thread across these items is the conversion of raw or curated sequence data into automated, reusable, and queryable infrastructure rather than new inferential methods. PePApipe integrates thirteen tools into a Python workflow for ASFV genome quality control, de novo assembly, and variant calling from raw reads, with SLURM execution. CAMP provides a Snakemake-based modular metagenomics system with standardized modules, summary reports, and Jupyter visualizations. The sewage resource curates 239 longitudinal samples from five European cities, offering metagenomic profiles, AMR genes, and MAGs through a PostgreSQL database. PaVarDB's BVbase Nextflow/Docker pipeline builds a missense variant database from raw Pseudomonas aeruginosa sequences, served via a Flask/MySQL interface. What is new is end-to-end coupling from raw sequence to queryable variant database in PaVarDB. The Eragrostis tef platform addresses accessibility and centralization only at a general level.
Published papers
A comprehensive database for biological data derived from sewage in five European cities.
Curated longitudinal dataset of 239 sewage samples from five European cities, with metagenomic profiles, AMR genes, MAGs, and a queryable PostgreSQL database.
PaVarDB: a database and web platform for missense variant analysis in Pseudomonas aeruginosa using an end-to-end BVbase pipeline.
PaVarDB presents BVbase, a Nextflow/Docker pipeline building a missense variant database from raw P. aeruginosa sequences, with a Flask/MySQL web interface for…
Developing a web-based platform for Eragrostis tef resource management and analysis.
Developing a web-based platform is beneficial for data accessibility, centralization, security, management, and scalability.
CAMP: a modular metagenomics analysis system for integrated multistep data exploration.
CAMP is a Snakemake-based modular metagenomics workflow with standardized modules, summary reports, and Jupyter visualizations for multistep analysis.
Preprints
'PePApipe': a complete bioinformatics analysis pipeline for African Swine Fever Virus genome
PePApipe is an automated, Python-based workflow integrating thirteen tools for ASFV genome QC, de novo assembly, and variant calling from raw reads, with SLURM…
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