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GA4GH Phenopacket Schema for computable representation of clinical phenotypic data. Build, validate, and convert phenopackets encoding patient phenotypes, diagnoses, genomic interpretations, and medic
Use with AI
Install the MCP server or CLI to instantly fetch Full phenopacket workflow documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/phenopackets
10x Genomics bamtofastq — converts Cell Ranger, Space Ranger, and Visium BAM files back to FASTQ format, preserving cell barcodes (CB), UMIs (UB), and read structure for re-processing with updated pip
1 shared topic • 3 shared operations
blue-crab converts Oxford Nanopore Technology (ONT) sequencing data between POD5 and SLOW5/BLOW5 file formats. Use for long-read genomics workflows that require SLOW5/BLOW5 input (e.g., Buttery-eel ba
1 shared topic • 3 shared operations
Loom — HDF5-based file format and Python library (loompy) for storing and accessing large single-cell RNA-seq datasets. Supports sparse/dense matrices, row attributes (genes/features), column attribut
1 shared topic • 3 shared operations
slow5lib and blue-crab — C library and Python tools for reading, writing, and converting Oxford Nanopore raw signal data in SLOW5/BLOW5 format. blue-crab converts between FAST5, POD5, and SLOW5/BLOW5
1 shared topic • 3 shared operations
twoBitToFa / faToTwoBit — UCSC Kent utilities for converting between the compact binary .2bit genome format and FASTA. twoBitToFa extracts sequences (full genome or specific regions) from a .2bit file
1 shared topic • 3 shared operations