Preprocessing pipeline
Pipeline workflow |
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Processing tools overview and limitations |
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| Software | Version | Download Link | Function | Limiation |
|---|---|---|---|---|
| bedtools | 2.30.3 | https://bedtools.readthedocs.io/en/latest | Genomic file formats conversion. | - |
| Bonito | 0.7.3 | https://github.com/nanoporetech/bonito | Base calling. | - |
| causalcall | - | https://github.com/scutbioinformatic/causalcall | Base calling. | Only for DNA. |
| CHEUI | - | https://github.com/comprna/CHEUI | RNA Modification detection. | Only for m6A and m5C. |
| Dorado | 0.5.3 | https://github.com/nanoporetech/dorado | Base calling, polyA detection, and modification detection. | - |
| Epinano | 1.2.0 | https://github.com/novoalab/EpiNano | RNA Modification detection. | - |
| Guppy | 6.0.1 | https://community.nanoporetech.com/downloads* | Base calling. | - |
| h5py | 1.8.18 | https://www.h5py.org | Pythonic interface to the HDF5 binary data format. | - |
| minimap2 | 2.24 | https://github.com/lh3/minimap2 | Aligns DNA/mRNA against the reference database. | - |
| MINES | - | https://github.com/YeoLab/MINES | RNA Modification detection. | Only for m6A. |
| m6Anet | 1.0 | https://github.com/GoekeLab/m6anet | RNA Modification detection. | Only for m6A. |
| Nanopolish | 0.14.0 | https://github.com/jts/nanopolish | Event segmeantation and alignment, modification and polyA detection. | - |
| Nanom6A | 2.0 | https://github.com/gaoyubang/nanom6A | RNA Modification detection. | Only for m6A. |
| ont-fast5-api | 4.0.2 | https://pod5-file-format.readthedocs.io | Nanopore sequencing data format conversion. | - |
| Rodan | - | https://github.com/biodlab/RODAN | Base calling. | Only for RNA. |
| SegPore | 1.0 | https://github.com/guangzhaocs/SegPore | Event segmeantation and alignment, modification detection. | - |
| Tailfindr | 0.14.0 | https://github.com/adnaniazi/tailfindr | PolyA detection. | - |
| Tombo | 1.5.1 | https://nanoporetech.github.io/tombo | Event segmeantation and alignment, modification detection. | - |
* Users need to register an account (for free) to download the software.