Skill UI

Automated guidance for SQL transform helper tasks within data pipelines, covering ETL, data transformation, workflow orchestration, and streaming, while following best practices, generating production-ready code, and validating results.

Direct REST API access to UniProt for searching proteins, fetching FASTA sequences, mapping identifiers, selecting annotations, and streaming large datasets within Python workflows.

polars-bio is a high-performance Python library built on Polars for genomic interval operations and bioinformatics file I/O. It provides a familiar DataFrame-centric API for interval arithmetic (overlap, nearest, merge, complement, etc.) and supports reading/writing major bioinformatics formats like BED, VCF, BAM, and GFF. Key features include streaming, cloud-native I/O, and SQL query support, making it a fast alternative for large-scale genomic data processing.

PySam provides a powerful Python interface for low-level, streaming access to HTSlib-supported genomic data formats. It enables reading, querying, filtering, and writing complex formats such as SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix-indexed tables. It is essential for bioinformatics pipelines requiring precise control over genomic data manipulation, including pileup and coverage calculations.