AgIn specifications


Unique identifier OMICS_12442
Name AgIn
Alternative name Aggregate on Intervals
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The program requires a modification.csv file as a primary input, which is produced by P_ModificationDetection module of SMRT Pipe.
Output data The GFF file reports all the predicted hypomethylated regions.
Biological technology Pacific Biosciences
Operating system Unix/Linux
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Yuta Suzuki

Publication for Aggregate on Intervals

AgIn citation


Centromere evolution and CpG methylation during vertebrate speciation

Nat Commun
PMCID: 5705604
PMID: 29184138
DOI: 10.1038/s41467-017-01982-7
call_split See protocol

[…] Methylation call from SMRT long reads was performed using AgIn algorithm, which is detailed in what follows. For methylation analysis, we used SMRT reads sequenced with P6-C4 chemistry and avoided mixing reads from different polymerase and chemistry, which i […]

AgIn institution(s)
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Pacific Biosciences, Menlo Park, CA, USA; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan; Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
AgIn funding source(s)
This work was supported in part by JSPS (Grant-in-Aid for JSPS Fellows 15J03645), by MEXT (Grants-in-Aid for Scientific Research 22129008 and 23241058 and by JST (CREST).

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