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proovread specifications

Information


Unique identifier OMICS_05092
Name proovread
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Output data High accuracy pacbio reads, trimmed for uncorrected/low quality regions, complete corrected pacbio reads including un-/ poorly corrected regions, ids of reads and the reason for excluding them from correction, annotations of potential chimeric joints clipped during trimming and the parameter set used for this run.
Biological technology Pacific Biosciences
Operating system Unix/Linux
Programming languages Perl
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Advanced
Version 2.12
Stability Stable
Requirements
NCBI Blast, samtools
Maintained Yes

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Maintainers


  • person_outline Frank Förster <>
  • person_outline Thomas Hackl <>

Publication for proovread

proovread in publications

 (21)
PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] coverage requirements and sequencing data that was available, with our goal being to generate the best possible contiguous and complete genome assembly, we tried both approaches. we initially used proovread () to error correct pacbio reads prior to assembly. this resulted in a loss of approximately 62% of sequenced pacbio bases (supplementary table s2). for comparison, we used […]

PMCID: 5868456
PMID: 29616001
DOI: 10.3389/fmicb.2018.00478

[…] insert size of 400 bp (ranging from 150 to 600 kb) on a hiseq sequencer (illumina, san diego, ca, united states). the paired-end short illumina reads were used to correct the long pacbio reads using proovread (), then the corrected pacbio reads were assembled de novo using smartdenovo., genomic dna from isolates gn26, gn28, and e20 was sequenced from a mate-pair libraries with an average insert […]

PMCID: 5788746
PMID: 29337073
DOI: 10.1016/j.cub.2017.11.060

[…] gene sequences. assembly and bioinformatics analyses was conducted in geneious version 9 (biomatters). error correction of long pacbio reads with short-read illumina data was performed using proovread []., promoter sequences were synthesized, subcloned into pgl3-basic (promega) and transformed into library efficiency dh5α competent cells (invitrogen). plasmids were extracted […]

PMCID: 5793194
PMID: 29346292
DOI: 10.3390/genes9010043

[…] isoforms is also improved with hiseq short reads []. in this case, certain programs have recently been developed such as pacbiotoca (error correction via celera assembler) [], lsc [], lordec [], and proovread []. pacbio long reads for phage, prokaryotic, and eukaryotic genome sequencing are corrected to 99.9% accuracy by pacbiotoca []. the computation method of lsc applies a homopolymer […]

PMCID: 5769442
PMID: 29334897
DOI: 10.1186/s12864-017-4430-y

[…] and a. aegerita aae-3-32 were also sequenced using a pacbio rs ii sequencing platform. pacbio reads of both the sibling strains were corrected with the help of illumina paired end reads using proovread []. illumina-corrected reads were further self-corrected using canu []. corrected pacbio reads of strain a. aegerita aae-3-13 were assembled using canu [] with an error rate set to 2.5%. […]


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proovread institution(s)
Department for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany; Department of Bioinformatics, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
proovread funding source(s)
Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP/20010-2015)/ERC Grant Agreement number 250194-Carnivorom.

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