polars-bio
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.
npx skills add K-Dense-AI/scientific-agent-skills --skill polars-bio --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# polars-bio ## Overview polars-bio is a high-performance Python library for genomic interval operations and bioinformatics file I/O, built on Polars, Apache Arrow, and Apache DataFusion. It provides a familiar DataFrame-centric API for interval arithmetic (overlap, nearest, merge, coverage, complement, subtract) and reading/writing common bioinformatics formats (BED, VCF, BAM, CRAM, GFF/GTF, FASTA, FASTQ). Key value propositions: - **6-38x faster** than bioframe on real-world genomic benchmarks - **Streaming/out-of-core** support for large genomes via DataFusion - **Cloud-native** file I/O (S3, GCS, Azure) with predicate pushdown - **Two API styles**: functional (`pb.overlap(df1, df2)`) and method-chaining (`df1.lazy().pb.overlap(df2)`) - **SQL interface** for genomic data via DataFusion SQL engine ## When to Use This Skill Use this skill when: - Performing genomic interval operations (overlap, nearest, merge, coverage, complement, subtract) - Reading/writing bioinformatics file formats (BED, VCF, BAM, CRAM, GFF/GTF, FASTA, FASTQ) - Processing large genomic datasets that don't fit in memory (streaming mode) - Running SQL queries on genomic data files - Migrating from bioframe to a
- Overview
- When to Use This Skill
- Quick Start
- Installation
- Basic Overlap Example
- Reading a BED File
- Core Capabilities
- 1. Genomic Interval Operations
- 2. Bioinformatics File I/O
- 3. SQL Data Processing
- 4. Pileup Operations
- Key Concepts
- Coordinate Systems
- Two API Styles
uv pip install "polars-bio==0.31.0" uv pip install "polars-bio[pandas]==0.31.0"
What does the polars-bio skill do?
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill polars-bio --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.