Preprocessing pipeline

  Pipeline workflow

NanoBaseLib preprocessing pipeline

  Processing tools overview and limitations

    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. -

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