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research software

nevelib

GitHub

Bioinformatics library

Sequence-analysis modules for Python research workflows.

nevelib provides read preparation, assembly support, homology search, clustering, multiple sequence alignment, and mapping as installable Python modules and focused CLIs. Research software can import what it needs without bundling these operations into each project.

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Current library profile

Scope
6 current module families
Interfaces
Focused CLIs and Python API
Runtime
Per-module YAML configs
Status
Alpha-stage 0.4.0

Downstream evidence only: nexteve-app uses nevelib as a dependency in a separate nrEVE analysis pipeline.

Context

Where this comes from

Who maintains the library and what research drives it.

Davide Colombo and the research context

nevelib is maintained by Davide Colombo, a third-year PhD candidate in biomedical engineering studying Aedes albopictus mosquito genomics — endogenous viral elements, transposable-element context, and piRNA-related analyses. The library extracts the reusable sequence-analysis code from that research into a shared layer.

Downstream projects add their own orchestration, thresholds, and biological interpretation on top. nevelib handles the lower-level operations they have in common.

Current module families

Module families

Six module families covering common sequence-analysis operations, each exposed as a CLI and a Python import.

nevelib.reads

Read preparation and QC

FASTQ extraction from alignments, trimming, compression, and read-level quality checks for sequencing data.

CLI nevelib-reads

Tools samtools, fastp, fastqc, pigz

nevelib.assembly

Assembly and contig refinement

Digital normalization, assembly support, coverage-based filtering, and deduplication for contig sets.

CLI nevelib-assembly

Tools bbnorm.sh, spades.py, mosdepth, blastn, samtools, pigz

nevelib.search

Homology search and hit interpretation

BLAST-based homology search, hit parsing, and filtering steps for sequence evidence review.

CLI nevelib-search

Tools blastn, blastx, makeblastdb

nevelib.clustering

Sequence clustering

MMseqs2 wrappers for collapsing or grouping related sequences in reusable downstream analyses.

CLI nevelib-clustering

Tools mmseqs

nevelib.msa

Multiple sequence alignment

MAFFT-backed alignment utilities for analyses that need reusable multiple sequence alignment steps.

CLI nevelib-msa

Tools mafft

nevelib.mapping

Reference and pairwise mapping

minimap2 execution and PAF parsing for reference-guided checks and pairwise mapping tasks.

CLI nevelib-mapping

Tools minimap2

Library boundary

What stays in the library and what doesn't

nevelib owns installable, testable sequence-analysis code. Workflow structure, biological thresholds, and interpretation belong to downstream projects.

Inside the current library

Concrete components, not a platform.

  • Six module families exposed as focused CLIs and Python imports.
  • Per-module YAML configs and explicit wrappers around standard bioinformatics tools.
  • Shared parsers and helpers for FASTA, FASTQ, BAM, TSV, and PAF handling.
  • Pytest-covered code intended for reuse across projects.