VTBuilder protocols

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VTBuilder specifications

Information


Unique identifier OMICS_24433
Name VTBuilder
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A single or paired end read data.
Input format FASTQ
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
JRE
Source code URL https://code.google.com/archive/p/vt-builder
Maintained Yes

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Maintainers


  • person_outline Simon Wagstaff <>
  • person_outline John Archer <>

Additional information


https://code.google.com/archive/p/vt-builder/

Publication for VTBuilder

VTBuilder in pipeline

2015
PMCID: 4488696
PMID: 26110505
DOI: 10.3390/toxins7062159

[…] in the sequencing reads. the distribution of open reading frames of cone snail toxin transcripts is indeed similar to the distribution of read lengths produced by 454 sequencing technology [,]. vtbuilder is a recently developed transcriptome assembler that considers relationships between co-evolving sites to avoid building chimeric transcripts, and has been shown to be effective […]

VTBuilder in publications

 (4)
PMCID: 5335903
PMID: 28130154
DOI: 10.1016/j.bbagen.2017.01.020

[…] a minimum window quality score of 20. after trimming, reads shorter than 10 bp were removed. processed paired-end read data were next assembled into contigs using the de novo transcriptome assembler vtbuilder executed with the following parameters: min. transcript length 150 bp; min. read length 150 bp; min. isoform similarity 96%. the isoform similarity parameter is a standard parameter […]

PMCID: 4552096
PMID: 26315097
DOI: 10.1186/s12864-015-1832-6

[…] seems to be that the trinity assembler is unable to deal effectively highly diversified families of large proteins, such as mps and sps. reassembly of both transcriptomes using the new assembler, vtbuilder, suggested assembling two pairs of these (pf_comp65_co_seq1 with pf_comp75_c0_seq1; pf_comp69_c0_seq1 with pf_comp72_c0_seq1), resulting in an estimated 7 p-iii mps. nonetheless, overall, […]

PMCID: 4488696
PMID: 26110505
DOI: 10.3390/toxins7062159

[…] in the sequencing reads. the distribution of open reading frames of cone snail toxin transcripts is indeed similar to the distribution of read lengths produced by 454 sequencing technology [,]. vtbuilder is a recently developed transcriptome assembler that considers relationships between co-evolving sites to avoid building chimeric transcripts, and has been shown to be effective […]

PMCID: 4662598
PMID: 26623194
DOI: 10.7717/peerj.1441

[…] 29/95 complete transcripts were identified respectively (). attempts have been made to develop an assembler specifically for samples containing large numbers of highly similar transcripts, such as vtbuilder (), although the current version has an upper limit of 5 million ≥ 120 bp reads, making it less suitable for the analysis of large-scale data generated from the most recent illumina […]

VTBuilder institution(s)
Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK
VTBuilder funding source(s)
Supported by the Leverhulme Trust, grant codes RPG-377 and RPG-2012-627.

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