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Protocols

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


download.png

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

 (65)
library_books

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

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

[…] engths, 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 were set […]

library_books

Draft genome of the Peruvian scallop Argopecten purpuratus

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

[…] tanus_v1.2.4 (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
Int J Genomics
PMCID: 5896239
PMID: 29785397
DOI: 10.1155/2018/7984292

[…] omplement 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. […]

library_books

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

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

[…] 6%) 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 Figure ). 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 inspection […]

library_books

Whole Genome Sequencing characterization of bloodstream infection causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374

2018
PMCID: 5955473
PMID: 29338592
DOI: 10.1080/21505594.2017.1421894

[…] led by using the PacBio HGAP3 workflow. Finally, the assembled contigs derived from the Miseq short reads were scaffolded with long PacBio reads, and then the resultant scaffolds were gap-filled with PBJelly []. The genome assembly was improved by Pilon []. Besides, the chromosomal replication origin (oriC) was predicted by OriFinder []. The circular chromosome was subsequently confirmed by using […]

call_split

The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees

2018
PLoS One
PMCID: 5755769
PMID: 29304093
DOI: 10.1371/journal.pone.0189738
call_split See protocol

[…] from the WGS-Assembler version 7 [] using the Illumina sequence reads. The resulting corrected reads were then used to improve and extend the 454/Roche contigs from the first step using the software PBjelly version 12.9.14 []. In order to optimize parameters of the assembly tools and to assess the quality of the final assembly we used the CEGMA tool [] to count the core eukaryotic genes. Higher n […]

Citations

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

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