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Use when working with cramino — a fast QC tool for long-read alignment files (CRAM and BAM). Generates alignment statistics including N50, median length, mean quality, percent aligned, and yield from
Use with AI
Install the MCP server or CLI to instantly fetch Cramino documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/cramino
HiCUP (Hi-C User Pipeline) is a modular pipeline for mapping and performing quality control on Hi-C sequencing data. Processes paired-end FASTQ reads through four stages: truncation at ligation juncti
1 shared topic • 2 shared operations
NanoPlot — visualization and quality-control tool for Oxford Nanopore long-read sequencing data. Generates read length histograms, quality distribution plots, cumulative yield curves, and alignment id
1 shared topic • 2 shared operations
PRINSEQ++ — high-performance C++ tool for quality control and preprocessing of FASTQ sequencing reads. Filters and trims reads by quality score, length, GC content, sequence complexity (DUST/entropy),
1 shared topic • 2 shared operations
PycoQC — Python tool for Oxford Nanopore sequencing QC that parses basecaller summary files (sequencing_summary.txt from Guppy, Dorado, or MinKNOW) and BAM alignment files to generate interactive HTML
1 shared topic • 2 shared operations
RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i
1 shared topic • 2 shared operations