harvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.
Tools
Parsnp - Core-genome...
Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which...
github.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...
github.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...
Geospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data,...
http://sandbox.bio - Learn how to use bioinformatics tools right from your browser.Everything runs in a sandbox, so you can experiment all you want.
More at sandbox.bio
bitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...
github.com - Create an interactive dot plot from mummer output OR PAF format
R script that makes a plotly interactive and/or static (png/pdf) dot plot.
Shiny app available for testing
yimingyu.shinyapps.io - shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package.
To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to...