Porechop specifications

Information


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

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Maintainer


  • person_outline Ryan Wick <>

Porechop in publications

 (7)
PMCID: 5920178
PMID: 29700153
DOI: 10.1128/genomeA.00321-18

[…] 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 () […]

PMCID: 5923466
PMID: 29614013
DOI: 10.3390/v10040172

[…] (ont). the result was then sequenced on a minion device, equipped with an r9.4 flowcell. for the data analysis, albacore v2.1 (ont, oxford, uk) was used for base-calling the reads, followed by porechop v0.2.1 (https://github.com/rrwick/porechop) in order to remove barcode sequences. genome map assembly was performed with canu v1.6 (https://github.com/marbl/canu) []. all the assembled […]

PMCID: 5909648
PMID: 29579234
DOI: 10.1093/femsle/fny069

[…] ead 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. […]

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

[…] 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 […]

PMCID: 5814496
PMID: 29449378
DOI: 10.1128/genomeA.00016-18

[…] 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 […]


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