nevelib.reads
Read preparation and QC
FASTQ extraction from alignments, trimming, compression, and read-level quality checks for sequencing data.
CLI nevelib-reads
External tools samtools, fastp, fastqc, pigz
Current package surface
What the library provides
Each module family corresponds to a package directory, a CLI entry point, and a set of external tool integrations.
Module families
Installed modules
All six module families are included in a base install.
nevelib.assembly
Assembly and contig refinement
Digital normalization, assembly support, coverage-based filtering, and deduplication for contig sets.
CLI nevelib-assembly
External 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
External tools blastn, blastx, makeblastdb
nevelib.clustering
Sequence clustering
MMseqs2 wrappers for collapsing or grouping related sequences in reusable downstream analyses.
CLI nevelib-clustering
External tools mmseqs
nevelib.msa
Multiple sequence alignment
MAFFT-backed alignment utilities for analyses that need reusable multiple sequence alignment steps.
CLI nevelib-msa
External tools mafft
nevelib.mapping
Reference and pairwise mapping
minimap2 execution and PAF parsing for reference-guided checks and pairwise mapping tasks.
CLI nevelib-mapping
External tools minimap2
Shared conventions
Common patterns across the current modules
Consistent interfaces and runtime behavior across all modules.
A sample YAML config per module
The repository currently ships six module-specific config samples, one for each installed capability family.
One CLI entry point per capability family
Each module is exposed through its own executable rather than a large monolithic command surface.
Importable Python functions
The same package can be used from application code when a downstream workflow needs direct composition.
External tools remain visible
Modules wrap common executables explicitly and fail clearly when expected tools are not available.
Dependencies
External tool requirements by module
Not every installation needs every executable. The required toolchain depends on which modules you actually plan to use.
| 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 |