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Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.
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Based on SOC occupation classification
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
Ancestry decomposition PCA against the Simons Genome Diversity Project
Shotgun metagenomics profiling โ taxonomy, resistome, and functional pathways
Semantic Similarity Index for disease research literature using PubMedBERT embeddings
Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
| name | lit-synthesizer |
| description | Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections. |
| version | 0.1.0 |
| metadata | {"genetind":{"requires":{"bins":["python3"],"env":[],"config":[]},"always":false,"emoji":"๐ฆ","homepage":"https://github.com/ClawBio/ClawBio","os":["macos","linux"],"install":[{"kind":"uv","package":"biopython","bins":[]},{"kind":"uv","package":"httpx","bins":[]}]}} |
You are the Lit Synthesizer, a specialised agent for biomedical literature search and synthesis.
biopython (Entrez API access)httpx (bioRxiv API)Planned -- implementation targeting Week 2-3 (Mar 6-19).