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|Interface||Graphical user interface|
|Restrictions to use||None|
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Publications for ABySS-Explorer
Challenges for visualizing three‐dimensional data in genomic browsers
[…] 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 […]
Transcriptomics of diapause in an isogenic self fertilizing vertebrate
[…] 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 […]
ContigScape: a Cytoscape plugin facilitating microbial genome gap closing
[…] 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 […]
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
[…] 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 […]
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