Run end-to-end bioinformatics analysis on marine genomic and metagenomic datasets.
npx skills add https://github.com/broomva/skills --skill ocean-genomics
Please help me install this Agent Skill. Skill: ocean-genomics Source: https://github.com/broomva/skills/tree/main/skills/science/ocean-genomics Command: npx skills add https://github.com/broomva/skills --skill ocean-genomics
This skill streamlines the complex, multi-step bioinformatics workflows required to analyze marine environmental DNA (eDNA), metagenomic data, and protein structures, reducing the barrier to entry for deep-sea biodiversity research.
Use the ocean-genomics skill to run the eDNA species inventory workflow on the sequencing files located in the current directory.
High-intent search queries and answers about installing and using this skill.
To process marine eDNA metabarcoding data, you can automate the transformation of raw FASTQ amplicon files into species lists and diversity metrics. This streamlines deep-sea biodiversity research by handling multi-step bioinformatics workflows in a single session.
Yes, you can predict 3D protein structures for novel marine enzymes using AI-driven foundation models like ESMFold2 and AlphaFold 3. This allows functional annotation and structural characterization directly within your metagenomic analysis workflow.
Yes, the pipeline supports shotgun metagenomic taxonomic profiling by orchestrating standard bioinformatics tools. It integrates with dependencies like samtools and minimap2 to process sequencing data and extract functional profiling insights.
Marine genomics analysis requires dependencies including biopython, biotite, gget, nextflow, samtools, minimap2, blast, and mmseqs2. These tools enable end-to-end processing of environmental DNA, metagenomic profiling, and protein structure prediction.
You can query marine databases during genomic data analysis by integrating with MCP servers. This allows the agentic bioinformatics workflow to dynamically query external marine databases and execute standard pipelines seamlessly.
The best way to analyze deep-sea expedition sequencing data is using an agentic bioinformatics workflow that handles eDNA metabarcoding, metagenomic profiling, and protein structure prediction. This reduces the barrier to entry for deep-sea biodiversity research.
openyakAutomate nf-core pipeline deployment and execution with Nextflow.
Runchuan-BUQuery the AlphaFold EBI API for UniProt protein structures and retrieve PDB/CIF files and confidence metrics.
yf8578Performs nucleotide and protein sequence similarity searches via NCBI BLAST+ locally or remotely.
pradyumnasagarParse, align, and quality-check bioinformatics sequences from FASTA, FASTQ, BAM, and VCF files.
