Table 1. Comparison between NanoR, poRe, IONiseR, poretools and HPG pore.
| Feature | NanoR | poRe | IONiseR | poretools | HPG Pore |
|---|---|---|---|---|---|
| Extract .fastq from .fast5 files* | ✔ | ✔ | ✔ | ✔ | ✔ |
| Extract .fasta from .fast5 files* | ✔ | ✔ | ✔ | ✔ | |
| Extract metadata from .fast5 files* | ✔ | ✔ | ✔ | ✔ | ✔ |
| Calculate/plot GC content* | ✔ | ✔ | |||
| Plot yield* | ✔ | ✔ | ✔ | ✔ | ✔ |
| Plot reads and base pairs number per time bin* | ✔ | ||||
| Plot min/mean/max reads quality and length per time bin* | ✔ | ||||
| Plot reads length versus reads quality* | ✔ | ||||
| Plot reads length histograms* | ✔1 | ✔ | ✔ | ✔ | |
| Plot reads quality histograms* | ✔2 | ||||
| Plot channels and muxes occupancy* | ✔ | ✔ | ✔3 | ||
| Plot reads and base pairs number per channel histograms* | ✔ | ✔ | |||
| Plot pass/fail/skip .fast5 files number and percentage* | ✔ | ||||
| Analyze GridION X5 outputs** | ✔ | ||||
| Analyze MinION/GridION X5 multi-read .fast5 files | ✔ | ||||
| Compare MinION/GridION X5 data | ✔ |
1 NanoR plots reads length histograms for each experiment when plotting reads length versus reads quality
2 NanoR plots reads quality histograms for each experiment when plotting reads length versus reads quality
3 Poretools does not plot muxes occupancy
* These features refers to MinION single-read data analysis
** poRe, IONiseR, poretools and HPG pore are not specifically designed to work with GridION X5 outputs; however, since from release 18.12.1 MinION and GridION X5 outputs are the same, theoretically these tools can work with GridION X5 single-read basecalled .fast5 files while they cannot work with default outputs from previous releases.