Metagenomic analysis pipelines and data visualization dashboards for Oxford Nanopore and Illumina sequencing data. Four Nextflow DSL2 pipelines cover real-time read processing, long-read assembly, short-read assembly, and downstream MAG analysis.
| Pipeline | Purpose | Key tools |
|---|---|---|
| nanopore_live | Real-time analysis during sequencing | Kraken2, Prokka/Bakta, HMMER3, DuckDB |
| nanopore_assembly | Long-read assembly + mapping + depth | Flye, metaMDBG, myloasm, minimap2, CoverM |
| illumina_assembly | Multi-assembler consensus assembly | Tadpole, Megahit, SPAdes, metaSPAdes, BBMap |
| mag_analysis | Downstream MAG analysis | 7-binner consensus, DAS Tool, Binette, 50+ processes |
git clone https://github.com/rec3141/danaSeq.git
cd danaSeq
# Real-time processing
cd nanopore_live
./install.sh && ./install.sh --check
./run-realtime.sh --input /path/to/nanopore/run --outdir /path/to/output \
--run_kraken --kraken_db /path/to/krakendb \
--run_prokka --run_sketch --run_tetra
# MAG analysis
cd ../mag_analysis
./install.sh && ./install.sh --check
./run-mag-analysis.sh \
--assembly /path/to/assembly.fasta \
--depths /path/to/depths.txt \
--outdir /path/to/output \
--db_dir /path/to/databases --all./download-databases.sh # Interactive menu
./download-databases.sh --human # Human reference (~4 GB)
./download-databases.sh --genomad --checkv --checkm2 --kaijuMIT. See LICENSE.
Repository: https://github.com/rec3141/danaSeq Documentation: https://rec3141.github.io/danaSeq/