minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome...2204 days ago
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 anno...linked maps can be explored using any web browser, allowing rapid genome...2204 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 optio...ne Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes...2195 days ago
2191 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 RNAseq...reads to be aligned against the reference genome and significantly improves ou...cies (e.g., Hyacinth macaw); Reference genome-...2191 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:...2040 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,...2188 days ago
Epiviz: an interactive visualization tool for functional genomics data.
...ve visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple...ns. It also includes data from the Gene Expression Barcode project for transcriptome visual...2185 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 (ANI...irs shared between two microbial genomes. FastANI supports pairwise c...eriments with complete and draft genomes, its accuracy is on par with...ANI Analysis of 90K Prokaryotic Genomes...2181 days ago
Genome U-Plot: a whole genome visualization
Genome U-Plot for producing clear and intuitive graphs that allows researchers to gener...chromoanagenesis events. The main features of the Genome U-Plot are its layered layout...thetic qualities. https://github.com/gaitat/GenomeU...2181 days ago