Read, write, and manipulate genomic data files via htslib.
npx skills add https://github.com/hxk622/TokenDance --skill pysam-hxk622
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/bioinformatics/pysam Command: npx skills add https://github.com/hxk622/TokenDance --skill pysam-hxk622
This Skill simplifies the complex task of reading, manipulating, and writing genomic data files, making bioinformatics analysis more accessible.
Use the pysam skill to read the first 1000 bases of chromosome 1 from the file 'reference.fasta'.
High-intent search queries and answers about installing and using this skill.
You can read and manipulate SAM/BAM and VCF files for NGS data analysis using a Pythonic interface to the htslib library. It enables efficient querying of genomic regions, calculation of read coverage, and integration into NGS data processing pipelines.
Extracting specific genomic regions from a FASTA sequence is best handled through a Pythonic interface to htslib. This approach enables efficient querying and extraction of target sequence regions directly within NGS data processing pipelines.
Yes, you can calculate read coverage depth from a BAM file using Python. A Pythonic interface to the htslib library provides the necessary functions to process alignments and compute coverage depth efficiently for NGS analysis.
Yes, pysam supports reading and writing CRAM alignments and BCF variants. It provides a Pythonic interface to the htslib library for seamlessly handling SAM, BAM, CRAM, VCF, and BCF genomic data files.
Analyzing variant calls from a VCF file in a bioinformatics pipeline is achieved through a Pythonic interface to htslib. It enables efficient reading, filtering, and manipulation of VCF/BCF variants alongside other genomic data formats.
ovachieverRetrieve nucleotide sequences and associated data from ENA via REST APIs.
robotlearning123Process genomic alignment, variant, and sequence files with pysam and htslib.
RamanEbrahimiProcess genomic alignment, variant, and sequence files for NGS analysis.
jaechang-hitsAccess and manipulate genomic data files via a Pythonic htslib interface.
