poretools 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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Documentation


Publication for poretools

poretools IN pipelines

 (13)
2018
PMCID: 5936980
PMID: 29760718
DOI: 10.3389/fgene.2018.00152

[…] raw sequence data were uploaded for base-calling using metrichor software (2d basecalling for sqkmap007 - v1.107). sequences in fasta format were extracted from the raw fast5 files using poretools v.0.6.0 (loman and quinlan, 2014). statistical analysis of the minion sequencing data were generated and visualized by de coster et al. (2017). in order to determine error rates, base-calls […]

2018
PMCID: 5936980
PMID: 29760718
DOI: 10.3389/fgene.2018.00152

[…] 2014). statistical analysis of the minion sequencing data were generated and visualized by de coster et al. (2017). in order to determine error rates, base-calls in fastq format were extracted using poretools v.0.6.0 (loman and quinlan, 2014) and then aligned against sanger sequenced reference using bwa-mem (version 0.7.12-41044), parameter “-x ont2d”. additional statistical analyses […]

2018
PMCID: 5940156
PMID: 29540443
DOI: 10.1534/g3.118.200087

[…] generated sequencing results in fast5 format. sequences that passed the protocol’s quality filter were converted from fast5 format to fasta format using poretools version 0.51 (loman and quinlan 2014; wei and williams 2016). the fasta files were processed with cutadapt version 1.14 to demultiplex the data using parameter (-o 20 –e 0.20 –m 50) (martin […]

2017
PMCID: 5524981
PMID: 28722025
DOI: 10.1038/ncomms16027

[…] r9.4 runs, reads that failed metrichor quality cutoffs were discarded as they also failed our alignment criteria. fast5 files generated by metrichor were converted into fastq and fasta formats using poretools (v0.5.1)55., for demultiplexing, index-sequences were aligned to the reads using blat with parameters: -nohead -stepsize=1 -minscore=20 -minidentity=20. reads for which index-sequences […]

2017
PMCID: 5563332
PMID: 28447221
DOI: 10.1007/s00401-017-1714-x

[…] chemistry and flo-map103/min104 flow cells were used for sequencing. base calling was done with the 2d plus barcoding protocol (metrichor, oxford, uk) after which fastq sequences were extracted with poretools v0.6.0 [33] according to the “best” protocol. sequencing reads were aligned to the human genome (hg19) with gmap v2016-06-30 [53] to account for splicing events. wild-type (wt), nonsense, […]

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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senaj

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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.