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

Name: DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation
Keywords: DNA methylation, methylation calling, long-read sequencing, nanopore sequencing, base modification

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 05 May 2021Publisher:Zenodo

Authors: Yang Liu; Wojciech Rosikiewicz; Ziwei Pan; Nathaniel Jillette; Ping Wang; Aziz Taghbalout; Jonathan Foox; +4 Authors

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

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Abstract

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 this article in Genome Biology: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02510-z

Related Organizations

University of Pennsylvania
United States
The JAX Cancer Center
United States
Weill Cornell Medicine
United States
St. Jude Children's Research Hospital
United States

Keywords

DNA methylation, methylation calling, long-read sequencing, nanopore sequencing, base modification

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