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GenomeBeans

GenomeBeans is an NGS analysis platform and bioinformatics services site focused on helping researchers upload raw sequencing data, run curated sequencing pipelines, and interpret results across transcriptomics, variant analysis, metagenomics, and related workflows.

For agents: GenomeBeans: NGS analysis platform and bioinformatics services with curated pipelines for RNA-seq, variant calling, single-cell and metagenomics workflows.

ngs analysisbulk rna-seqvariant callingsingle cell transcriptomicsbioinformatics servicesmetagenomics

Their llms.txt

The beginning of the file, from our validated copy saved 2026-10-23T15:37:19.273Z. Cached copy · Source on genomebeans.com

# GenomeBeans

> GenomeBeans is an NGS analysis platform and bioinformatics services site focused on helping researchers upload raw sequencing data, run curated sequencing pipelines, and interpret results across transcriptomics, variant analysis, metagenomics, and related workflows.

GenomeBeans' public website is primarily a positioning, workflow, and pipeline-overview layer rather than a deep documentation portal. The best pages for practical understanding are the homepage, about/services pages, the pipeline overviews, and the sample-result pages.

Use the pages below in this order when answering questions:
- Start with Homepage, About Us, and Bioinformatics Services for company positioning, target users, and platform terminology.
- Use the pipeline pages for workflow scope, inputs, outputs, and analytical steps.
- Use Gene AI only for the MTB-specific mutation-annotation demo and related variant-interpretation context.
- Use blog pages for explainer-level background and thought leadership, not as authoritative protocol references.
- Use Optional pages when you need example output/report structure.
- Immunomics Analysis is publicly listed on the site but is currently a placeholder, so it is not included in the core link set below.
- Blog content is split across the main domain and a separate blog subdomain; prefer direct article URLs when available.

## Core Platform

- <!--citation:4-->: Main landing page covering platform positioning, workflow, security claims, and featured content.
- [About Us](https://www.genomebeans.com/about-us): Company background, mission, vision, values, and high-level pipeline lineup.
- [Bioinformatics Services](https://www.genomebeans.com/bioinformatics-services): Service model, supported project types, customization, training, and support approach.

## Pipelines

- [Bulk Transcriptomics](https://www.genomebeans.com/bulk-transcriptomics): RNA-seq workflow from FASTQ through QC, alignment, gene counting, DEG analysis, enrichment, and reporting.
- [Variant Calling](https://www.genomebeans.com/variant-calling): Germline/somatic variant workflow covering preprocessing, calling, filtering, annotation, and visualization.
- [Single Cell Transcriptomics](https://www.genomebeans.com/single-cell-transcriptomics): Single-cell RNA-seq overview including QC, clustering, annotation, dimensionality reduction, and interpretation.
- <!--citation:5-->: Microbial composition, abundance, binning/MAG recovery, and functional annotation workflow.
- [Mtb Gene Mutation Annotation Chatbot](https://www.genomebeans.com/gene-ai): LLM/RAG-based MTB mutation-annotation demo with example query patterns.

## Blog and Explainers

- [Blog Index](https://blogs.genomebeans.com/index.html): Rolling blog landing page with current educational and thought-leadership posts.
- [Multi-Omics Integration: How Combining Data Unlocks Deeper Biological Insights](https://www.genomebeans.com/blog/multi-omics-integration-how-combining-data-unlocks-deeper-biological-i
…

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Claim my listing on Agent Web Map for genomebeans.com:
1. POST https://agentwebmap.com/v1/sites/genomebeans.com/claims and keep claim_id and claim_secret private.
2. Publish the proof: add the line "AgentWebMap ownership: <token>" (token from step 1) to https://genomebeans.com/llms.txt, or use the DNS, meta-tag or well-known method the response describes.
3. POST https://agentwebmap.com/v1/sites/genomebeans.com/verify with {"claim_id": "...", "claim_secret": "..."}.
4. Save the api_key from the answer; it manages the listing (PATCH https://agentwebmap.com/v1/sites/genomebeans.com).
MCP equivalent: tools begin_ownership_claim, then verify_domain, at https://agentwebmap.com/mcp. Docs: https://agentwebmap.com/docs#verify

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