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Porechop specifications


Unique identifier OMICS_17306
Name Porechop
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Output data It will output the trimmed reads to stdout and print its progress info to stderr.
Output format FASTA, FASTQ
Biological technology Oxford Nanopore
Operating system Unix/Linux, Mac OS
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Ryan Wick

Porechop citations


Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing

Genome Announc
PMCID: 5920178
PMID: 29700153
DOI: 10.1128/genomeA.00321-18

[…] eads were obtained, for a total of 1,214 Mbp (130× coverage) and an average length of 8,737 bp. Fast5 files were base called using Albacore version 2.0.2. Passed reads were trimmed for adapters using PoreChop version 0.2.3 and then assembled using SMARTdenovo version 1.0 (https://github.com/ruanjue/smartdenovo). Contigs obtained from the assembly were polished using Racon version 0.5.0 () and Nano […]


Community led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

FEMS Microbiol Lett
PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069
call_split See protocol

[…] (50> read length <250), and for trimming (phred score < 28) (Andrews ). Basecalling of the Nanopore reads was performed with the software Albacore v2.1.3 from ONT, and the barcodes were removed using Porechop. Read length distribution and quality of the Nanopore reads was assessed using NanoPlot.The genome was first assembled with SPAdes, version 3.11.1 using default parameters (Bankevich et al.) […]


Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

Microb Genom
PMCID: 5885017
PMID: 29547094
DOI: 10.1099/mgen.0.000165

[…] to a separate Linux server, where bases were called using ONT's Albacore command line tool (v1.0.1), using barcode demultiplexing and fastq output. Adapter sequences were trimmed from the reads using Porechop (v0.2.0, https://github.com/rrwick/Porechop), with barcode demultiplexing, and only keeping reads where Albacore and Porechop agreed on the barcode bin, to prevent cross-barcode contamination […]


Complete Genome Sequences of Six Listeria monocytogenes Sequence Type 9 Isolates from Meat Processing Plants in Norway

Genome Announc
PMCID: 5814496
PMID: 29449378
DOI: 10.1128/genomeA.00016-18
call_split See protocol

[…] to ∼8,000-kb fragments in a Covaris g-TUBE, and sequencing was performed on a FLO-MIN107 flow cell. Raw fast5 reads were base-called using ont-albacore version 1.2.2, and adapters were removed using Porechop version 0.2.1. For the reads from barcoded libraries, both ont-albacore and Porechop were run with barcode demultiplexing. The genomes were assembled using the Unicycler version 0.3.0b hybrid […]


Whole Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia

Genome Announc
PMCID: 5754500
PMID: 29301891
DOI: 10.1128/genomeA.01424-17
call_split See protocol

[…] encing libraries from total DNA. One R9.4 MinION flow cell was used for six multiplexed DNA samples. Base calling of MinION sequences was performed using Albacore v1.1.0, and adapters were removed by Porechop (https://github.com/rrwick/Porechop).The hybrid de novo assembly of Illumina and Nanopore reads was done using Unicycler v0.3.1 (). We performed separate assemblies of Illumina reads relating […]

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