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
Related persons:
- 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
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