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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
Use with AI
Install the MCP server or CLI to instantly fetch 10x Genomics bamtofastq documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/bamtofastq
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
GA4GH Phenopacket Schema for computable representation of clinical phenotypic data. Build, validate, and convert phenopackets encoding patient phenotypes, diagnoses, genomic interpretations, and medic
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