Read, write, and manipulate FASTA, GenBank, and FASTQ biological sequence files.
npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill sequence-io
Please help me install this Agent Skill. Skill: sequence-io Source: https://github.com/dakesan/cc-dnawork-plugin/tree/main/scientific-skills/sequence-io Command: npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill sequence-io
This Skill simplifies working with biological sequence files across FASTA, GenBank, and FASTQ formats. It also provides indexed access to large FASTA references and handy sequence operations to streamline genomics workflows.
Read sequences from 'reference.fasta' and print basic metadata (IDs and lengths).
High-intent search queries and answers about installing and using this skill.
This Skill automates reading, writing, and converting across FASTA, GenBank, and FASTQ formats using Biopython. Load sequences from any supported format, then write to another—enabling rapid format conversion for genomics pipelines without manual parsing.
Yes. The Skill provides indexed random access to large FASTA files via faidx, enabling fast extraction of specific regions without loading the entire file into memory—critical for NGS workflows and reference-based analyses at scale.
The Skill includes built-in operations to compute complement, reverse complement, and translate DNA/RNA sequences to protein. Apply these transformations directly within your workflow to derive derived sequences and reading frames.
It supports FASTA, GenBank, and FASTQ formats with coordinate awareness (0-based and 1-based) and integrates with pysam for NGS pipelines and BLAST workflows, ensuring interoperability across downstream genomics tools.
The Skill leverages faidx indexing for efficient random access to large FASTA references. Index creation and management are integrated, allowing you to query specific genomic regions without preprocessing.
Yes. The Skill handles batch file I/O for sequences, enabling you to calculate metrics like GC content across many FASTA, GenBank, or FASTQ files efficiently within a single workflow.
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