github.com - PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It...
academic.oup.com - ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing...
github.com - The Genome Context Viewer (GCV) is a web-app that visualizes genomic context data provided by third party services. Specifically, it uses functional annotations as a unit of search and comparison. By adopting a common set of annotations, data-store...
biit.cs.ut.ee - g:Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces. We provide at least 40 types of IDs for more than 60 species. The 98 different namespaces supported for human include Ensembl,...
https://proksee.ca/ - Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.
search.carrot2.org -
This is the demo application of the Carrot2 clustering engine. It uses Carrot2's algorithms to organize search results into thematic folders.
User interfaces
Web Search Clustering organizes search results from public...
researchrabbitapp.com - You’re determined students, passionate teachers, and inspired creators of everything we know! Yet, all the researchers we spoke with over the past year uncovered the same reality:
Despite the degrees you’ve earned, the effort and...
carpentries-incubator.github.io - Introduction to Bioinformatics workflows with Nextflow and nf-core
Getting Started with Nextflow
Objectives Understand
What a workflow management system is.
Understand the benefits of using a workflow management system.
Explain the benefits of...
github.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...
daehwankimlab.github.io - Resource for downloading all the HISAT2 related files
Please cite:
Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915...