ONT QC PipelineA quality-control and preliminary assembly pipeline for Oxford Nanopore Technologies (ONT) whole-genome sequencing data from bacterial isolates. It calculates read statistics, identifies species with Kraken2, estimates genome size with LRGE, and assembles genomes using Autocycler with Flye fallback. Final assemblies are additionally checked for plasmid matches with Plassembler. The pipeline produces combined QC summaries covering sequencing depth, taxonomic composition, assembly size and contig count.Versions

v0349482 (default)

Tags: nanopore, quality control, bacteria, genome assembly, autocycler, kraken2, cpgParameters

samples (file, multiple) required: Input ONT R10 bacterial isolate reads in fastq.gz format. Provide one FASTQ file per sample.

Links

Documentation

GitHub repository

License: MIT

Open ONT QC Pipeline in the CPG Portal. Configuring and running a tool needs JavaScript.