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Use when working with MIP (Medical Information Process) — a workflow management system for clinical whole-genome and whole-exome sequencing analysis. Runs end-to-end rare disease (rd_dna, rd_rna) and
Use with AI
Install the MCP server or CLI to instantly fetch MIP documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/mip
Java command-line tools from the Broad Institute for manipulating high-throughput sequencing data and formats including BAM, CRAM, and VCF.
2 shared topics • 3 shared operations
IGV (Integrative Genomics Viewer) — high-performance Java desktop application for interactive visualization and exploration of genomic data. Supports BAM/CRAM alignments, VCF variants, BED/GFF annotat
2 shared topics • 2 shared operations
Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage
2 shared topics • 2 shared operations
Sarek — nf-core Nextflow pipeline for germline and somatic variant calling from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing data. Supports multiple variant cal
2 shared topics • 2 shared operations
sigmap is a C++ tool for signal-level alignment of nanopore sequencing data, mapping raw electrical signals (squiggles) directly to a reference genome without basecalling. Uses Dynamic Time Warping (D
2 shared topics • 2 shared operations