Modalysis: DNA Methylation Analysis from Long Read Oxford-Nanopore Sequencing Data

Arnav Bharti, Priyanka Roy, Tanmaya Mahapatra, Sanjay Kumar Kochar, Dhanpat Kumar Kochar, and Ashis Das

Product Demo

Product walkthrough of Modalysis running on long-read Oxford-Nanopore sequencing data.

Documentation

Access full project documentation at modalysis.arnavbharti.com.

Related Citation

Additional publication link: https://rdcu.be/e7iFr

Abstracts of the 9th International Conference on Plasmodium vivax Research (ICPvR) 2025

Malaria Journal (2025), 24(1), 423.

Published: December 1, 2025 | ISSN: 1475-2875

DOI: 10.1186/s12936-025-05498-0

Sample .modalysis Snippets

The following snippets are taken from the output of the program on our own data.

DMR_common_genes.modalysis

ROW_TYPE	MANIFESTATION	REGION	MODIFICATION_A	MODIFICATION_B	COMMON_GENE_COUNT	GENE_ID	EXPRESSION_STATUS
SUMMARY	CM	PROMOTER	5MC	5MC_5HMC	93		
GENE	CM	PROMOTER	5MC	5MC_5HMC		PVX_002760	NDE
GENE	CM	PROMOTER	5MC	5MC_5HMC		PVX_003635	NDE
GENE	CM	PROMOTER	5MC	5MC_5HMC		PVX_080155	NDE
GENE	CM	PROMOTER	5MC	5MC_5HMC		PVX_080265	NDE

DMR_common_genes_5mC_CM_vs_HD.modalysis

ROW_TYPE	MODIFICATION	REGION	MANIFESTATION_A	MANIFESTATION_B	COMMON_GENE_COUNT	GENE_ID	EXPRESSION_STATUS_A	EXPRESSION_STATUS_B
SUMMARY	5MC	PROMOTER	CM	HD	6			
GENE	5MC	PROMOTER	CM	HD		PVX_082870	DOWN	NDE
GENE	5MC	PROMOTER	CM	HD		PVX_082900	NDE	NDE
GENE	5MC	PROMOTER	CM	HD		PVX_084462	NDE	NDE
GENE	5MC	PROMOTER	CM	HD		PVX_087950	NDE	NDE

DMR_common_genes_5mC_5hmC_CM_vs_HD.modalysis

ROW_TYPE	MODIFICATION	REGION	MANIFESTATION_A	MANIFESTATION_B	COMMON_GENE_COUNT	GENE_ID	EXPRESSION_STATUS_A	EXPRESSION_STATUS_B
SUMMARY	5MC_5HMC	PROMOTER	CM	HD	3			
GENE	5MC_5HMC	PROMOTER	CM	HD		PVX_000755	NDE	NDE
GENE	5MC_5HMC	PROMOTER	CM	HD		PVX_089310	DOWN	NDE
GENE	5MC_5HMC	PROMOTER	CM	HD		PVX_114370	NDE	NDE
SUMMARY	5MC_5HMC	BODY	CM	HD	18

HD_5mC.modalysis

CHROMOSOME	START	END	MODIFICATION	N_VALID_COV	N_MOD	TOTAL_FILES	N_FILES
PV_SAL1_CHR01	3658	3659	m	5	0	4	2
PV_SAL1_CHR01	3791	3792	m	5	0	4	2
PV_SAL1_CHR01	9974	9975	m	5	1	4	3
PV_SAL1_CHR01	10046	10047	m	5	0	4	3
PV_SAL1_CHR01	10168	10169	m	5	0	4	3

DMR_UNC_vs_CM_5mC_5hmC_annotated.modalysis

CHROMOSOME	START	END	SCORE	MAP_BASED_P_VALUE	EFFECT_SIZE	PCT_A_SAMPLES	PCT_B_SAMPLES	A_H_M_COUNTS	A_VALID_COVERAGE	B_H_M_COUNTS	B_VALID_COVERAGE	A_N_MOD	B_N_MOD	PROMOTER	BODY	ENHANCER
PVAD80_MIT	1606	1607	2.8711949699505297	0.03376251969586922	0.2655172413793103	60	100	h:6,m:0	20	h:1,m:0	29	6	1	PVAD80_MIT0001		
PV_SAL1_CHR01	102079	102080	4.305730070664809	0.007743890200090922	0.7777777777777778	60	100	h:7,m:0	9	h:0,m:0	5	7	0		PVX_087745	
PV_SAL1_CHR01	102248	102249	5.3374960031411405	0.0024833594111452924	-0.875	60	100	h:0,m:1	8	h:0,m:5	5	1	5		PVX_087745	
PV_SAL1_CHR01	117451	117452	2.935921457815006	0.03821150012151597	-0.46153846153846156	60	100	h:0,m:0	8	h:0,m:6	13	0	6			PVX_087750