Can I use this for real-time coverage calculation?

Yes, the skill supports pileup analysis which allows for efficient base-by-base coverage and read depth calculations across specific genomic regions.

Can I run samtools commands directly through this skill?

Yes, the skill provides a direct Python wrapper for samtools and bcftools, allowing you to run commands like sort, index, and view from within your script.

Does it require pre-indexed files?

For random access (fetching specific regions), index files such as .bai, .tbi, or .fai are required; however, the skill can still read files sequentially without indices.

Does this skill handle 0-based or 1-based coordinates?

Pysam uses 0-based, half-open coordinates for its Python API, consistent with Python's slicing, while handling internal conversion for 1-based formats like SAM and VCF.

Pysam Genomic Toolkit

Name: Pysam Genomic Toolkit
Author: K-Dense-AI

byK-Dense-AI

•

2,188

数据科学与机器学习

Manipulates genomic datasets including SAM, BAM, VCF, and FASTA files through a Pythonic interface to htslib.

关于

Pysam equips Claude with the expertise to handle complex Next-Generation Sequencing (NGS) data formats. It enables programmatic reading, writing, and filtering of alignment files, variant records, and reference sequences. Ideal for bioinformaticians and researchers, this skill streamlines tasks like calculating coverage, performing pileup analysis, and managing coordinate systems (0-based vs 1-based), while providing integrated access to samtools and bcftools utilities for high-performance genomic data processing.

主要功能

Advanced pileup analysis for coverage and base-level statistics
Efficient random access to FASTA and FASTQ sequence files
Comprehensive SAM, BAM, and CRAM alignment manipulation
Integrated wrappers for samtools and bcftools commands
VCF and BCF variant file reading, writing, and filtering
2,188 GitHub stars

使用场景

Filtering and annotating genetic variants for population studies
Automating NGS data processing and bioinformatics pipelines
Performing quality control and depth-of-coverage analysis

关于

主要功能

Advanced pileup analysis for coverage and base-level statistics
Efficient random access to FASTA and FASTQ sequence files
Comprehensive SAM, BAM, and CRAM alignment manipulation
Integrated wrappers for samtools and bcftools commands
VCF and BCF variant file reading, writing, and filtering
2,188 GitHub stars

使用场景

Filtering and annotating genetic variants for population studies
Automating NGS data processing and bioinformatics pipelines
Performing quality control and depth-of-coverage analysis