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ABySS-Explorer specifications

Information


Unique identifier OMICS_00873
Name ABySS-Explorer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Version 1.3.4
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publications for ABySS-Explorer

ABySS-Explorer citations

 (4)
library_books

Challenges for visualizing three‐dimensional data in genomic browsers

2017
FEBS Lett
PMCID: 5638070
PMID: 28771695
DOI: 10.1002/1873-3468.12778

[…] m , Space Syntax , and Route‐Zooming , among others. The sequence coordinates themselves can be abstracted to adapt to other data, (e.g., by stacking regions or focusing only on transcript scopes ). ABySS‐Explorer adds granularity to permit visual accentuation of the sequence . The sequence can also be arranged nonlinearly represented as a Hilbert graph, a fractal arrangement of the coordinates w […]

library_books

Transcriptomics of diapause in an isogenic self fertilizing vertebrate

2015
BMC Genomics
PMCID: 4657215
PMID: 26597228
DOI: 10.1186/s12864-015-2210-0

[…] 0 cycles. Reads with Q < 30 were trimmed by using Trimmomatic software [], whereas reads with Q >30 were used to create de novo genome assembly via the ABySS assembler []. N50 values as visualized by ABySS-Explorer [, ] serve as a quality control for the assemblies that were built successfully using various k-mers: k = 32, 40, 48, 56, 58, 60, and 64 [].Once a reference genome or transcriptome was […]

library_books

ContigScape: a Cytoscape plugin facilitating microbial genome gap closing

2013
BMC Genomics
PMCID: 3651407
PMID: 23627759
DOI: 10.1186/1471-2164-14-289

[…] me-level overview, ABySS-Explorer [] and TGNet [] were developed. TGNet incorporates several scripts for converting transcripts to facilitate assembly and represents contigs graphically using points. ABySS-Explorer [] is another global viewer of contig assembly. However, neither program was designed to treat repeat contigs or display the reads that link contigs and imply the location of gaps and r […]

library_books

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

2012
BMC Plant Biol
PMCID: 3413510
PMID: 22548759
DOI: 10.1186/1471-2229-12-61

[…] equences, or specific regions in a whole genome assembly. As confirmation of the validity of our procedure, another group has successfully assembled another genome using this tool []. A similar tool, ABySS-Explorer has been developed for assemblies generated by ABySS []. However, our results demonstrate the utility of shotgun 454 sequences with a size of 300–500 nt, making the experiment cost effi […]

Citations

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ABySS-Explorer institution(s)
BC Cancer Agency, Genome Sciences Centre

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