nf-core pipeline ·
nf-core/mitodetect
A Nextflow pipeline for end-to-end analysis of mitochondrial next-generation sequencing data.
What nf-core/mitodetect is
nf-core/mitodetect is a bioinformatics pipeline designed to carry out end-to-end analysis of mitochondrial next-generation sequencing (NGS) data.
Originally written by tm4zza within the nf-core community framework, it helps researchers process sequencing reads and evaluate data quality for mitochondrial studies.
What the pipeline does
The pipeline ingests sequencing read files specified via an input sample sheet. It performs initial quality control checks on raw reads using FastQC, followed by aggregate quality control reporting using MultiQC.
Key facts
- Pipeline engine
- Nextflow
- Original author
- tm4zza
- Included tools
- FastQC, MultiQC
- Primary input format
- CSV sample sheet pointing to FASTQ files
What you can use it for
- Mitochondrial sequencing read quality assessment
- Inspect raw sequencing quality profiles across mitochondrial NGS datasets using FastQC.
- Aggregated QC reporting
- Compile batch-level read statistics and quality visualisations into a consolidated MultiQC report.
Run it here
The research agent runs nf-core/mitodetect with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Standardises raw quality control and reporting across mitochondrial sequencing runs.
- Integrates into the nf-core and Nextflow reproducible workflow environment.
Watch out for
- Downstream variant calling or specialised mitochondrial processing steps beyond initial QC are not detailed in the available documentation.
Questions
Can I run nf-core/mitodetect without my own cluster?
The research agent runs nf-core/mitodetect with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/mitodetect under?
MIT, like every nf-core pipeline.
What inputs does the pipeline accept?
It accepts a CSV sample sheet pointing to input sequencing reads (FASTQ files).
Which tools handle the quality control steps?
Raw read quality control is conducted with FastQC, and aggregated reports are compiled using MultiQC.
Can custom pipeline parameters be supplied in configuration files?
No, pipeline parameters must be provided via the command-line interface or a Nextflow params file rather than custom configuration files.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/mitodetect's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.