Read, write, and query indexed genomic alignment, variant, and sequence files.
npx skills add https://github.com/dralkh/seerai --skill pysam-dralkh
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/dralkh/seerai/tree/main/skills/pysam Command: npx skills add https://github.com/dralkh/seerai --skill pysam-dralkh
Pysam removes the friction of working directly with genomic file formats by giving you a Pythonic way to read, write, filter, and query alignment, variant, and sequence data.
Use the pysam skill to open your indexed genomic file, fetch a target region, and summarize the reads, variants, or sequences it contains.
High-intent search queries and answers about installing and using this skill.
To fetch reads from a genomic region in a BAM file using Python, you can open the indexed file and query the target coordinates. This approach enables region extraction, read inspection, and coverage calculation for specific genomic intervals.
Yes, you can extract reference sequences from a FASTA file for specific intervals. By querying the indexed FASTA file, you retrieve the exact reference bases needed for tasks like variant validation or sequence comparison.
The best way to inspect genotypes and INFO fields in a VCF file is to parse it programmatically with a Python genomic library. You can read records, filter variants based on specific criteria, and extract sample genotype data directly for summarization.
Pileup analysis works with both CRAM and BAM files. The processing logic supports reading and querying alignment files in both formats, allowing you to perform pileup analysis and calculate coverage across indexed CRAM or BAM inputs.
You can query tabix-indexed BED, GTF, and GFF annotation files by opening them with a Pythonic genomic interface. This exposes tabix workflows, allowing you to fetch overlapping features and integrate annotations with variant or alignment data.
biomaps-infraRead, manipulate, and write genomic data files via a Python interface.
OwnLabAIIngest and query genomic variant data using TileDB-VCF.
Imad-OuteCreate statistical graphics in Python using seaborn and matplotlib.
Imad-OuteManage and analyze BAM, CRAM, VCF, BCF, FASTA, and FASTQ genomic files.
