Published May 5, 2021 | Version 1.0
Software Open

DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation

Creators

  • 1. The Jackson Laboratory for Genomic Medicine
  • 2. Center for Applied Bioinformatics, St. Jude Children's Research Hospital
  • 3. Department of Physiology and Biophysics, Weill Cornell Medicine
  • 4. Department of Medicine, University of Pennsylvania
  • 5. The Jackson Laboratory Cancer Center

Contributors

  • 1. The Jackson Laboratory for Genomic Medicine

Description

NANOME Github repository

https://github.com/TheJacksonLaboratory/nanome

File list

  • nanome.zip: Source code of paper, also available at GitHub https://github.com/TheJacksonLaboratory/nanome.
  • C.tar.gz: The genome motif generated for DeepMod paper (https://www.nature.com/articles/s41467-019-10168-2) cluster model in 5mC prediction in human genome.
  • genome-annotation.tar.gz: Genome annotation files.
  • model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+.tar: DeepSignal (doi:10.1093/bioinformatics/btz276) methylation-calling model files sample.
  • megalodon_model.tar.gz: Megalodon model configuration files sample from https://github.com/nanoporetech/megalodon.
  • ecoli.tar.gz: Reference genome of E. coli.
  • hg38.tar.gz: Reference genome of human.
  • hg38_chr22.tar.gz: A small reference genome of human for chromosome 22.
  • coli_data_from_meteore.tar.gz: E. coli data (50 reads) from METEORE paper (https://www.nature.com/articles/s41467-021-23778-6).
  • ecoli_fast5_test.tar.gz: E. coli data (selected 10 reads) from METEORE paper (https://www.nature.com/articles/s41467-021-23778-6).

*Correspondence should be addressed to S.L. (sheng.li@jax.org).

Please cite our article: 

Liu, Y., Rosikiewicz, W., Pan, Z. et al. DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. Genome Biol 22, 295 (2021). https://doi.org/10.1186/s13059-021-02510-z

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02510-z 

Files

nanome.zip

Files (10.6 GB)

Name Size Download all
md5:27e0d4ce9b6b2d05e69633abaed9f5b3
3.3 GB Download
md5:eba31c15a5523f8eece55891f0d51f5a
6.7 MB Download
md5:628685cbfd8cb495c102e2aa6ec76167
110.4 MB Download
md5:402d5541730c4142b05aff7192891db8
20.4 MB Download
md5:be75735d9d94a20fba9f950e9af644e5
2.5 GB Download
md5:7403b2401b1f2d5f7b5f47eb80d5859f
4.3 GB Download
md5:df186900d4409a07aa07f9aab471db11
65.1 MB Download
md5:73a436b5c66240a0029074e5a1e9d341
87.2 MB Download
md5:527d1e4b2d3c3fa1887a1e4ba5460a1f
196.1 MB Download
md5:fe762dc3404824324e47d2688176d289
28.3 MB Preview Download
md5:675fce14183e23fa97b8284a545add25
15.4 kB Download