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Protocols

poretools specifications

Information


Unique identifier OMICS_07584
Name poretools
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FAST5
Output format FASTQ/FASTA
Biological technology Oxford Nanopore
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
HDF5, R, rpy, h5py
Maintained Yes

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Versioning


No version available

Documentation


Publication for poretools

poretools citations

 (38)
call_split

Unbiased Strain Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field forward Biosurveillance Protocol

2018
Sci Rep
PMCID: 5883038
PMID: 29615665
DOI: 10.1038/s41598-018-23641-7
call_split See protocol

[…] Nanopore reads were basecalled using the local basecalling algorithm in MinKNOW version 1.4.3. FAST5 files of basecalled reads were converted to FASTA files using poretools. The FASTA files from each sequenced sample (4.1 and 1.1) were queried for EVEV/VEEV using several kmer-based metagenomics taxonomy callers, including Kraken, Kaiju, and Centrifuge. Family-l […]

library_books

Identification of potential regulatory mutations using multi omics analysis and haplotyping of lung adenocarcinoma cell lines

2018
Sci Rep
PMCID: 5862974
PMID: 29563587
DOI: 10.1038/s41598-018-23342-1

[…] y MinION Mk 1B with the SpotON Flow Cell (FLO-MIN106, R9.4 version for 2D; FLO-MIN107, R9.5 version for 1D and 1D2, Oxford Nanopore Technologies).FASTQ files were generated from the FAST5 files using poretools. Sequences were mapped using bwa-mem with ont2d settings for 2D reads (H1975, RERF-LC-KJ) and default settings for 1D and 1D2 reads (LC2/ad).MinION reads were considered if mapping quality s […]

library_books

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

2018
Sci Rep
PMCID: 5816649
PMID: 29453452
DOI: 10.1038/s41598-018-21484-w

[…] We used Metrichor 2.42.2 to basecall our 1D and 2D data. Poretools 0.6.0 was used to convert FAST5 files from Metrichor into FASTQ files for mapping. Statistics were also collected using Poreminion 0.4.4 and fast5tools 0.1. We compared Metrichor with the ne […]

library_books

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

2018
Nat Commun
PMCID: 5803254
PMID: 29416032
DOI: 10.1038/s41467-018-03016-2

[…] Raw ONT reads (fastq) were extracted from base-called FAST5 files using poretools. Overlaps were generated using minimap with the recommended parameters (-Sw5 -L100 -m0). Genome assembly graphs (GFA) were generated using miniasm. Unitig sequences were extracted from GFA f […]

library_books

Complete Nucleotide Sequence of an Escherichia coli Sequence Type 410 Strain Carrying blaNDM 5 on an IncF Multidrug Resistance Plasmid and blaOXA 181 on an IncX3 Plasmid

2018
Genome Announc
PMCID: 5794949
PMID: 29437102
DOI: 10.1128/genomeA.01542-17

[…] ee libraries were run in a MinION Mk1B according to the manufacturer’s instructions (Oxford Nanopore Technologies [ONT]) and base called with ONT’s Metrichor software. Fastq files were extracted with Poretools version 0.6.0 (). Unicycler version 0.4.0 was used for a hybrid assembly of the MiSeq data (), which was manually corrected using Genomics Workbench version 10.1.1 (Qiagen). The genome was a […]

library_books

Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity

2018
PLoS One
PMCID: 5774705
PMID: 29351296
DOI: 10.1371/journal.pone.0189993

[…] ring and trimming using Sickle and were quality corrected with BayesHammer before being assembled de novo. 2D MinION reads were extracted using the Metrichor Agent and FASTQ file were generated using PoreTools v5.0.Illumina reads were assemble de novo either alone or in combination with MinION reads using SPAdes 2.9.0, in the standerd mode or in hybrid mode with the nanopore option, respectively. […]

Citations

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poretools institution(s)
Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA

poretools review

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Desktop
Poretools is relatively easy to use those with command-line experience. This software produces easy to understand summary plots of MinION data. The output is more intuitive that the output from Oxford Nanopore's MinKnow software.