CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence ann...inked maps can be explored using any web browser, allowing rapid genome browsin...2207 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with opt...Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and de...2198 days ago
2194 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAse...ads to be aligned against the reference genome and significantly improves ou...es (e.g., Hyacinth macaw); Reference genome-free -...2194 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Cre...2042 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and th...2191 days ago
Epiviz: an interactive visualization tool for functional genomics data.
Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplo...2188 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (AN...rs shared between two microbial genomes. FastANI supports pairwise c...riments with complete and draft genomes, its accuracy is on par with...ANI Analysis of 90K Prokaryotic Genomes Reveal...2183 days ago
Genome U-Plot: a whole genome visualization
Genome U-Plot for producing clear and intuitive graphs that allows researchers to gene...chromoanagenesis events. The main features of the Genome U-Plot are its layered layout...hetic qualities. https://github.com/gaitat/GenomeUPlot2183 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently e...1490 days ago