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Pychopper — Nanopore direct cDNA read preprocessing tool that identifies, orients, and trims full-length reads using primer detection (pHMM or alignment). Rescues fused reads by dynamic programming, e
Use with AI
Install the MCP server or CLI to instantly fetch Pychopper documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/pychopper
BAMtools — C++ API and command-line toolkit for reading, writing, sorting, indexing, filtering, merging, splitting, and converting BAM alignment files. Provides JSON-based filter expressions, multi-fo
2 shared topics • 2 shared operations
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
2 shared topics • 2 shared operations
VSEARCH — open-source, multithreaded alternative to USEARCH for amplicon and metagenomics sequence analysis. Performs dereplication, chimera detection (de novo and reference-based), OTU/ASV clustering
2 shared topics • 2 shared operations
Bracken (Bayesian Reestimation of Abundance with KrakEN) — statistical method for computing species-level abundance estimates from Kraken/Kraken2/KrakenUniq taxonomic classifications. Redistributes re
2 shared topics • 1 shared operation
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
2 shared topics • 1 shared operation