分析ONT数据有哪些软件？

这篇文章中罗列了关于Nanopore数据的分析软件，比较全面，可以参考下。


软件

Computational tools for ONT data analysis

Data analysis

Computational tool

Base calling

ONT’s (https://github.com/nanoporetech/)

Guppy, Metrichor, Nanonet, Albacore, Scrappie, Flappie, Taiyaki, Bonito

Third party

Nanocall46, Chiron70, Causalcall35, DeepNano47, DeepNano-blitz246, basecRAWller247, WaveNano248, MinCall249, URnano250, CATCaller251, SACall252, Halcyon253, Fast-Bonito254

Quality control

Prealignment

NanoPack65, LongQC255, PycoQC256, MinIONQC257, RabbitQC258, NanoR63, poRe60, pyPore66

Postalignment

AlignQC42, SQANTI3259, NanoOK61, pyPore

Processing and visualization

Processing

Tombo (https://github.com/nanoporetech/tombo), Poretools64, HPG pore62

Visualization

SquiggleKit260, BulkVis49, Methylartist261, NanoMethViz262, Methplotlib263

DNA modification detection

5mC (CpG)

Nanopolish75, Megalodon (https://github.com/nanoporetech/megalodon), DeepSignal77, Tombo, Guppy, DeepMod76, SignalAlign71, NanoMod78

5mC (GpC)

Nanopolish, NP-SMLR72

6mA

Guppy, Tombo, mCaller174, NanoMod, DeepMod, DeepSignal

5hmC, 4mC

SignalAlign (5hmC), Tombo (4mC)

RNA modification detection

m6A

EpiNano73, xPore264, MINES84, Nanocompore265, Nanom6A266, Yanocomp267, ELIGOS83, DRUMMER268, Tombo

Pseudouridine (Ψ), m5C

nanoRMS (Ψ)104, Tombo (m5C)

Error correction

Hybrid (graph based)

FMLRC93, LoRDEC91, Jabba269, ECTools270, HG-ColoR271, NaS272, Ratatosk273

Hybrid (alignment based)

pacBioToCA274, LSC90, Nanocorr45, proovread275, Hercules276, PBcR274

Hybrid (dual alignment/graph based)

HALC92, ColorMap277

Self

Canu88, daccord278, LoRMA89, MECAT279, pbdagcon280, FLAS281, MARVEL282, NanoReviser283

Splice-aware

TALC (hybrid)284, iSONcorrect (self)285

Genome alignment

Minimap2 (ref. 96), GraphMap95, NGMLR98, LAST97, BWA-MEM286, BLAST94, LRA287, Winnowmap2 (ref. 288), MashMap2 (ref. 289), NanoBLASTer290, mapAlign291, GraphAligner292, smsMap293, lordFAST294, S-conLSH295, QAlign296

Splice-aware

Minimap2, GraphMap2 (ref. 102), GMAP100, STAR101, deSALT103, Magic-BLAST297, Deep-Long298, uLTRA299

Genome assembly

Canu, Miniasm107, Flye110, Redbean/wtdbg2 (ref. 111), Falcon-Unzip300, Shasta164, Raven301, NextDenovo (https://github.com/Nextomics/NextDenovo), Peregrine302, HINGE303, TULIP304, NECAT305

Metagenome tailored

metaFlye306, OPERA-MS (hybrid)106

Haplotype-aware

Hifiasm307

Genome polishing

Nanopolish, Racon308, Medaka (https://github.com/nanoporetech/medaka), NeuralPolish309, PEPPER-Margin-DeepVariant310, NextPolish (https://github.com/Nextomics/NextPolish), POLCA311, HomoPolish38

SV detection

Sniffles98, SVIM312, NanoSV112, Picky33, NanoVar113, Dysgu313, SENSV314, cuteSV315

SNV detection

LongShot116, DeepVariant310, iGDA316, Nanopanel2 (ref. 317), Clair318

Haplotyping

WhatsHap117, Medaka, HapCUT2 (ref. 319), flopp320, DR2S321, Nanopanel2, iGDA, Clair

Repetitive element analysis

Non-reference transposable element detection

TLDR118, PALMER322, TELR (https://github.com/bergmanlab/TELR)

Tandem repeat

TRiCoLOR119, STRique323, NanoSatellite207

Transcriptome construction and quantification

De novo

RATTLE129, CARNAC-LR324, isONclust325, IDP-denovo (hybrid)128

Reference genome guide

IDP (hybrid)127, TALON126, FLAIR123, StringTie2 (ref. 125), FLAMES326

Quantification only

LIQA327, AERON328, Mili (https://github.com/Augroup/Mili)

Transcriptome characterization

Alternative splicing

FLAIR

Gene fusion

IDP-fusion (hybrid)329, JAFFAL330, AERON, LongGF331

Circular RNA

CIRI-long170

Poly(A) tail length

Nanopolish

Allele-specific expression

IDP-ASE (hybrid)332, LORALS333

Experimental assays for ONT applications

Application

Experimental assay

Genomics

Amplicon sequencing

NanoAmpli-seq334, Dual-UMI-tagging335

Targeted genome sequencing

nCATS336, CATCH197

Epigenomics

DNA methylation and chromatin accessibility

MeSMLR-seq72, SMAC-seq175, nanoNOMe176

Nucleosome occupancy

MeSMLR-seq

Histone modification

DiMeLo-seq181, BIND&MODIFY182

3D genome structure

Pore-C180

Protein–DNA interaction mapping

DiMeLo-seq, Nanopore-DamID337

DNA replication (replication fork detection)

D-Nascent179, FORK-seq338

Single-cell transcriptome

ScCOLOR-seq339, ScISOr-Seq340, scNaUmi-seq341, FLT-seq326

Epitranscriptomics (RNA secondary structure)

PORE-cupine184, SMS-seq342

RNA metabolism (nascent RNA detection)

Nano-ID186, nano-COP343

• 3D, three dimensional; SNV, single nucleotide variation.