DeepMP – Detect DNA modifications in Nanopore Sequencing data

DeepMP

:: DESCRIPTION

DeepMP is a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a read is methylated or not.

::DEVELOPER

DeepMP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Python

:: DOWNLOAD

DeepMP

:: MORE INFORMATION

Citation:

Bonet J, Chen M, Dabad M, Heath S, Gonzalez-Perez A, Lopez-Bigas N, Lagergren J.
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.
Bioinformatics. 2021 Oct 28:btab745. doi: 10.1093/bioinformatics/btab745. Epub ahead of print. PMID: 34718417.

NanoMethViz 1.2.0 – Visualise Methlation data from Oxford Nanopore Sequencing

NanoMethViz 1.2.0

:: DESCRIPTION

NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon.

::DEVELOPER

Shian Su

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R package / BioConductor

:: DOWNLOAD

NanoMethViz

:: MORE INFORMATION

Citation

Su S, Gouil Q, Blewitt ME, Cook D, Hickey PF, Ritchie ME.
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.
PLoS Comput Biol. 2021 Oct 25;17(10):e1009524. doi: 10.1371/journal.pcbi.1009524. Epub ahead of print. PMID: 34695109.

NanoARG – Antimicrobial Resistance analysis for Nanopore reads

NanoARG

:: DESCRIPTION

NanoARG is an free web resource for the analysis of antibiotic resistance genes in metagenomes from environmental samples using the MinION nanopore sequencing technology.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Arango-Argoty GA, Dai D, Pruden A, Vikesland P, Heath LS, Zhang L.
NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes.
Microbiome. 2019 Jun 7;7(1):88. doi: 10.1186/s40168-019-0703-9. PMID: 31174603; PMCID: PMC6555988.

NanoMark – DNA Assembly Benchmark for Nanopore long reads

NanoMark

:: DESCRIPTION

NanoMark is a system for benchmarking DNA assembly tools, based on 3rd generation sequencers.

::DEVELOPER

NanoMark team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 NanoMark

:: MORE INFORMATION

Citation

Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads.
Sović I, Križanović K, Skala K, Šikić M.
Bioinformatics. 2016 May 9. pii: btw237.

DeepMod v0.1.3 – Deep-learning tool for DNA Methylation Detection on Nanopore data

DeepMod v0.1.3

:: DESCRIPTION

DeepMod is a computational tool which takes long-read signals as input and outputs modification summary for each genomic position in a reference genome together with modification prediction for each base in a long read.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DeepMod

:: MORE INFORMATION

Citation

Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K.
Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.
Nat Commun. 2019 Jun 4;10(1):2449. doi: 10.1038/s41467-019-10168-2. PMID: 31164644; PMCID: PMC6547721.

NanoMod 0.2.2 – Detect DNA Modifications using Nanopore long-read Sequencing data

NanoMod 0.2.2

:: DESCRIPTION

NanoMod is a novel computational tool for the detection of DNA modifications using Nanopore long-read sequencing data. The evaluation on simulation data with different types of modifications and on a methylation data of E. coli suggested that NanoMod achieved better performance than other existing tools in detecting modifications without training data.

::DEVELOPER

Wang Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Pyton

:: DOWNLOAD

NanoMod

:: MORE INFORMATION

Citation

Qian Liu, Daniela C. Georgieva, Dieter Egli and Kai Wang.
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data.
BMC Genomics 20(1):78, 2019. doi: 10.1186/s12864-018-5372-8.

NanoOK 1.33 – Alignment and Analysis of Nanopore Reads

NanoOK 1.33

:: DESCRIPTION

NanoOK is a tool from TGAC for alignment and analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ files, align them (with a choice of alignment tools), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / VirtualBox
  • Java

:: DOWNLOAD

  NanoOK

:: MORE INFORMATION

Citation:

NanoOK: Multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.
Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP.
Bioinformatics. 2015 Sep 17. pii: btv540

Poretools 0.6.0 – A Toolkit for Analyzing Nanopore Sequence data

Poretools 0.6.0

:: DESCRIPTION

Poretools is a flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 Poretools

:: MORE INFORMATION

Citation:

Poretools: a toolkit for analyzing nanopore sequence data.
Loman NJ, Quinlan AR.
Bioinformatics. 2014 Aug 20. pii: btu555.

HPG pore – Framework for Nanopore Sequencing data

HPG pore

:: DESCRIPTION

HPG Pore is a toolkit to explore and analyze nanopore sequencing data that can run both on a single computer and on the Hadoop distributed computing framework.

::DEVELOPER

HPG pore team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

 HPG pore

:: MORE INFORMATION

Citation:

HPG pore: an efficient and scalable framework for nanopore sequencing data.
Tarraga J, Gallego A, Arnau V, Medina I, Dopazo J.
BMC Bioinformatics. 2016 Feb 27;17(1):107. doi: 10.1186/s12859-016-0966-0.

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