nevelib

A modular Python bioinformatics library for genomic sequence analysis.

Six module families — read preparation, assembly, homology search, clustering, multiple sequence alignment, and mapping — exposed as focused CLIs and importable Python modules.

Requires Python ≥ 3.11.

Website: nevelib-website.vercel.app

Installation

pip install nevelib              # all six modules
pip install nevelib[viz]         # adds matplotlib, seaborn
pip install nevelib[confirm]     # adds pysam
pip install nevelib[all]         # viz + confirm
pip install nevelib[dev]         # all + pytest, pytest-cov

Modules

Module	Description	CLI
reads	BAM → FASTQ extraction, quality trimming, QC reporting	nevelib-reads
assembly	Digital normalization, de novo assembly, coverage filtering, deduplication	nevelib-assembly
search	BLAST-based homology search, hit parsing, filtering, classification	nevelib-search
clustering	Sequence clustering via MMseqs2	nevelib-clustering
msa	Multiple sequence alignment via MAFFT	nevelib-msa
mapping	Pairwise and reference alignment via minimap2	nevelib-mapping

Usage

Each module is invoked with a YAML configuration file:

nevelib-reads config.yaml
nevelib-assembly config.yaml
nevelib-search config.yaml
nevelib-clustering config.yaml
nevelib-msa config.yaml
nevelib-mapping config.yaml

Sample configs ship with each module. To copy one out:

python3 -c "import nevelib.reads; print(nevelib.reads.__path__[0])"
# then copy config.sample.yaml from the printed path

Modules are also importable directly:

from nevelib.search.blast import run_blastn
from nevelib.clustering.mmseqs import run_mmseqs_linclust
from nevelib.msa.mafft import run_mafft

External tool requirements

Each module wraps standard bioinformatics tools that must be available on PATH:

Module	Required tools
reads	samtools, fastp, fastqc, pigz
assembly	bbnorm.sh (BBTools), spades.py, mosdepth, blastn, samtools, pigz
search	blastn, blastx, makeblastdb
clustering	mmseqs
msa	mafft
mapping	minimap2

License

MIT