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PBSuite specifications

Information


Unique identifier OMICS_21465
Name PBSuite
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 15.8.24
Stability Stable
Maintained Yes

Subtools


  • PBHoney
  • PBJelly

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Adam C. English <>

Additional information


https://sourceforge.net/p/pb-jelly/wiki/Home/?#058c

Publications for PBSuite

PBSuite citations

 (81)
library_books

Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double strand breaks

2018
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] in the backbone contigs were detected and modified by picard (http://broadinstitute.github.io/picard/), gatk, and perl scripts. the contigs were further improved using the gap-closing module in pbjelly (pbsuite 15.8.24), and the sequences were corrected once again with the miseq data as described above. each of the contigs from yph499 and s799 were sorted and renamed after s288c annotation […]

library_books

A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination

2018
PMCID: 5940159
PMID: 29602812
DOI: 10.1534/g3.118.200154

[…] 23, 25, 27, 31, 33, 35 and 37, with best assembly achieved at k-mer value 35. the jellyfish algorithm was implemented for k-mer counting (). uncorrected pacbio reads were used to fill in gaps using pbjelly2 (). local misassemblies and any detected incorrect bases were corrected and polished using pilon (). scaffolds less than 500 bp in size were discarded to create a final draft assembly ()., […]

library_books

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

2018
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] filtering options, and coverages were explored, but the reported parameters were chosen since they produced the longest contigs and scaffolds. this assembly was then used as the reference for pbjelly [] version 15.8.24, a program used to incorporate pacbio sequences., pacbio sequences were removed from the dataset if they were shorter than 5,000 bp. the blasr [] settings in pbjelly […]

library_books

Draft genome of the Peruvian scallop Argopecten purpuratus

2018
PMCID: 5905365
PMID: 29617765
DOI: 10.1093/gigascience/giy031

[…] (platanus, rrid:scr_015531) [], and the gaps were then filled by gapcloser_v1.12-r6 (gapcloser, rrid:scr_015026) []. subsequently, the pacbio data were used for additional gap filling by pbjelly_v14.1 (pbjelly, rrid:scr_012091) with default parameters [], and then all of the illumina reads were used to correct the genome assembly by pilon_v1.18 (pilon, rrid:scr_014731) for two rounds […]

library_books

Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing

2018
PMCID: 5896239
PMID: 29785397
DOI: 10.1155/2018/7984292

[…] tool in the fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). we assembled the resulting contigs again using soapdenovo2 and mapped the pacbio rsii read data to long scaffolds using pbjelly [] to remove sequence gaps., we mapped the amberjack genome sequence onto the yellowtail rh physical map []. then, we used the sequences of the mapped markers of yellowtail for blast searches […]

library_books

Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single Molecule Real Time sequencing

2018
PMCID: 5854607
PMID: 29545612
DOI: 10.1038/s41598-018-23053-7

[…] were corrected (hgap seed length cutoff: 4 kb) and assembled resulting in 48 contigs. seven contigs (total size ~4.46 mb) showed markedly higher coverage depth (>190-fold, supplementary figureĀ ). pbjelly (pbsuite 14.9.9) was used to perform scaffolding and subsequent gap-filling on this set of contigs employing all reads in the high coverage bin, producing five contigs total. manual […]


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PBSuite institution(s)
Human Genome Sequencing Center at Baylor College of Medicine, Houston, TX, USA

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