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...2196 days ago
2192 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-...2192 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,...2189 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 scatter...2186 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
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 independent...1488 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopoli...lculate an improved consensus sequence for a draft genome assembly, detect base modific..., call SNPs and indels with respect to a reference genome...2169 days ago