Read and write genomic data files via a Pythonic htslib interface.
npx skills add https://github.com/Yezez9/Research-Agent --skill pysam-yezez9
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/pysam Command: npx skills add https://github.com/Yezez9/Research-Agent --skill pysam-yezez9
This Skill provides a powerful Python interface for reading, manipulating, and writing common genomic file formats, streamlining bioinformatics workflows.
Use the pysam skill to read the first 1000 bases of chromosome 1 from the reference.fasta file.
High-intent search queries and answers about installing and using this skill.
To read specific genomic regions from a BAM file, this Skill provides a Pythonic interface to htslib, enabling indexed access for random retrieval of alignment data within targeted loci. It supports efficient querying of large sequencing files.
Yes, you can extract variants from a VCF file. This Skill processes variant call formats, allowing you to query specific genomic coordinates and manipulate genetic variant data efficiently using a Pythonic interface.
The best way to process large FASTQ files is using sequential processing capabilities. This Skill interfaces with htslib to read and write sequence files, enabling efficient manipulation of raw reads for next-generation sequencing analysis.
Yes, this Skill supports reading and writing CRAM files. It provides a comprehensive interface to htslib for handling sequencing alignment data across SAM, BAM, and CRAM formats, streamlining bioinformatics workflows.
You can fetch a reference sequence for a particular locus from a FASTA file using indexed access. This Skill enables random retrieval of genomic regions, allowing you to extract specific sequences from reference genomes efficiently.
You can analyze coverage depth by reading the BAM file and querying the specific genomic region. This Skill enables indexed access for random retrieval, allowing you to calculate sequencing coverage across targeted loci efficiently.
SologaRead, write, and manipulate genomic data files in SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ formats.
jaechang-hitsFilter, merge, annotate, and extract genetic variants in VCF and BCF files.
qinyan-aiProcess SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ files via Python.
jaechang-hitsAccess and manipulate genomic data files via a Pythonic htslib interface.
