Process BAM, VCF, and FASTA genomics data with Python via htslib.
npx skills add https://github.com/mkurman/tamux --skill pysam-mkurman
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/mkurman/tamux/tree/main/skills/scientific-skills/pysam Command: npx skills add https://github.com/mkurman/tamux --skill pysam-mkurman
Pysam provides a Pythonic interface to the htslib library, enabling researchers to read, write, and manipulate genomic alignment, variant, and sequence data without diving into low-level tooling.
Install pysam and load a BAM to fetch reads, iterate variants, and access reference sequences.
High-intent search queries and answers about installing and using this skill.
You can read and filter BAM files in Python by using a Pythonic interface to htslib, which enables region queries and statistical analyses on sequencing alignment data without low-level tooling.
Processing VCF variant data in a Python bioinformatics pipeline is best handled by wrapping htslib, allowing you to iterate variants, apply filters, and compute statistics directly within Python workflows.
Yes, you can query specific genomic regions from FASTA reference sequences using Python by leveraging htslib wrappers that provide efficient access to reference sequence data for extraction and analysis.
Yes, pysam supports CRAM files alongside BAM and SAM formats for sequencing alignment workflows, providing a Pythonic interface to read, write, and manipulate genomic alignment data efficiently.
Calculating sequencing depth and coverage statistics from BAM files in Python is done through htslib wrappers that enable querying and computing statistical analyses directly on alignment data.
Before running genomic data queries with pysam, you need Python installed along with pysam and related index files for your BAM, VCF, or FASTA data to ensure reliable region queries and filtering operations.
qinyan-aiProcess SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files via Python.
ovachieverRead and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.
tassiovaleManipulate biological sequences, alignments, trees, and diversity metrics in Python.
jaechang-hitsAccess and manipulate genomic data files via a Pythonic htslib interface.
