nose-pipeline 1.0.1

NOSE — Novel Species Identification Pipeline (Computational Systems Biology Lab @ IIT Madras)

NOSE — Novel Species Identification Pipeline

Computational Systems Biology Lab @ IIT Madras

A modular Snakemake toolkit for identifying and characterizing novel microbial species from genome assemblies.

📖 Full Documentation  ·  🐛 Report an Issue  ·  📦 Pipeline Code

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What is NOSE?

NOSE takes a directory of genome FASTA files and returns — with full scientific evidence — whether each genome belongs to an already-described species or is a candidate novel organism.

FASTA Files → M1: QC & Taxonomy → M2: Novelty Screen → Novel / Known
                                                              ↓
                                          M3: Phylogenetic Tree
                                          M4: Metagenome Mapping
                                          M5: Functional Annotation
                                          M6: Metabolic Modeling

Module	What it does	Key output
M1	Assembly QC + taxonomy (QUAST, CheckM2, GTDB-Tk)	genome_summary.csv
M2	ANI / AAI / POCP against RefSeq type strains	potential_novel.csv
M3	ML phylogenetic trees (GToTree + IQ-TREE)	Newick + iTOL files
M4	Metagenome abundance mapping (sylph)	final_report.csv
M5	Functional annotation (Prokka, antiSMASH, ABRICATE)	functional_summary.csv
M6	Metabolic model reconstruction (CarveMe, MEMOTE)	SBML + model_summary.csv

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Installation

1. Install the CLI package

pip install nose-pipeline

2. Clone the pipeline

git clone https://github.com/RamanLab/NOSE.git
cd NOSE

3. Set up conda + Snakemake

nose-setup

Installs Miniconda3 if needed, creates a snakemake conda environment with Snakemake ≥ 8.

4. Download databases

nose-db

Downloads CheckM2, GTDB-Tk, EukCC, and CAT databases as needed.

5. Launch the web UI

nose-ui

Opens http://localhost:5050 — fill in paths, click Run Module.

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CLI Commands

Command	Description
nose-ui	Start the web UI (default port 5050)
nose-setup	Install conda environment
nose-db	Download databases
nose-info	Show version, env status, paths

nose-info        # check everything is set up correctly
nose-ui --port 8080 --no-browser   # custom port, skip browser open
nose-setup --env-name myenv        # custom env name
nose-db --skip-gtdbtk              # skip the 66 GB GTDB-Tk download

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System Requirements

• OS: Linux, macOS, or Windows (WSL2)
• Python: ≥ 3.9
• Conda: Miniconda3 or Anaconda (auto-installed by nose-setup if missing)
• RAM: ≥ 16 GB recommended (GTDB-Tk loads ~66 GB DB)
• Disk: ≥ 100 GB for all databases

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Developed by

Computational Systems Biology Lab @ IIT Madras

• 🌐 ramanlab.github.io/NOSE
• 📁 github.com/RamanLab/NOSE

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License

MIT License — see LICENSE