Table 1 RNA modification detection tools for direct RNA sequencing data sequenced with ONT
From: The RMaP challenge of predicting RNA modifications by nanopore sequencing
RNA detection method | Tested RNA modifications | Method approach | Ref. |
|---|---|---|---|
nanoRMS/nanoRMS2 | ψ, Nm, m6A | Direct & signal comparison | |
EpiNano | m6A, ψ, m2G, m7G, m3U | Signal comparison & error-profile | |
m6anet | m6A | Direct | |
Magnipore | any | Signal comparison | |
xPore | m6A | Signal comparison | |
Yanocomp | m6A | Signal comparison | |
Nanocompore | m6A, Ino, ψ, m5C, m62A, m1G | Signal comparison | |
ELIGOS | m6A, m1A, m5C, hm5C, f5C, m7G, Ino, ψ, 5moU | Signal comparison & error-profile | |
JACUSA2 | m6A | Signal comparison | |
Tombo | any | Signal comparison & direct | ONT |
Nanom6A | m6A | Direct | |
DENA | m6A | Direct | |
mAFiA | m6A | Direct | |
Penguin | ψ | Direct | |
MINES | m6A | Direct | |
Nano-ID | e5U, Br5U, I5U, S4U, S6G | Direct | |
DRUMMER | m6A | Error-profile | |
DiffErr | – | Error-profile | |
CHEUI | m6A, m5C | Direct | |
NanoPsu | ψ | Direct | |
NanoSPA | ψ, m6A | Direct | |
TandemMod | m1A, m6A, m5C, m7G, hm5C | Direct | |
IL-AD | m1A, m6A, m5C, 5mC, 5hmC, ψ | Direct | |
nanoDoc | ψ, m7G, m5C, Cm, Gm, m6A, m1A, m2G, m5U … | Direct | |
ModiDeC | m6A, ψ, Ino, Gm, m1A | Direct |
