https://academic.oup.com/database/article/doi/10.1093/database/baw084/2630454

Address of the bookmark: http://ani.mypathogen.cn/

Address of the bookmark: https://github.com/vpc-ccg/haslr

Canu is a hierachical assembly pipeline which runs in four steps:

• Detect overlaps in high-noise sequences using MHAP
• Generate corrected sequence consensus
• Trim corrected sequences
• Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

Address of the bookmark: https://github.com/marbl/canu

“It’s like a subway map,” she said, “but for DNA.”

That idea is exactly what Sequence Tube Map brings to life.

Instead of showing a genome as one long, confusing sequence, it displays different genomic paths like routes on a metro map. Where sequences are shared, the paths travel together. Where genetic variation occurs, they branch into different routes and may join again later.

This makes complex genome graphs much easier to explore.

Maya could now see how different haplotypes moved through the same genomic region and where they took different paths. She could even view sequencing reads mapped onto the graph, helping her understand what was happening in regions with genetic variation.

What once looked like a tangled network now looked like a journey.

Sequence Tube Map turns the complexity of graph genomes into a visual story—making it easier for scientists to see how DNA can take different routes.

Read more at  https://github.com/vgteam/sequencetubemap 

and

https://academic.oup.com/bioinformatics/article/35/24/5318/5542397

Demo at https://vgteam.github.io/sequenceTubeMap/

https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

Common uses of the tool include:

• Displaying the sequence and/or genes in a GenBank flat file.
• Highlighting differences and/or similarities in gene content between related organisms.
• Comparing SNPs and indels between closely-related strains or serovars.
• Comparing gene expression values across multiple samples or timepoints.
• Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

• Builds on BioPerl and the input file formats that it supports, including:
  • GenBank flat files, GFF, FASTA
• Accepts a number of other commonly-used datatypes and file formats:
  • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
• Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
• Requires only a single configuration file whose layout mirrors that of the figure itself.
  • Predefined configuration files and "track" types are supplied for common datasets.
  • Advanced features allow limited analyses to be performed as a figure is drawn.
• Includes an extensive set of regression tests.
• Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn