2195 days ago
RNA-seq Analysis Workshop Course Materials
...ly divided into two "types": Reference genome-based - an assembled genome exists for a species for whic...reads to be aligned against the reference genome and significantly improves ou...cies (e.g., Hyacinth macaw); Reference genome-free - no genome assembly for...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:...2043 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...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 then constructs a novel...2192 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...2189 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...ignment-free computation of whole-genome Average Nucleotide Identity (...airs shared between two microbial genomes. FastANI supports pairwise c...periments with complete and draft genomes, its accuracy is on par with...t ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Bounda...2184 days ago
Genome U-Plot: a whole genome visualization
Genome U-Plot for producing clear and intuitive graphs tha...d chromoanagenesis events. The main features of the Genome U-Plot are its layered layout...sthetic qualities. https://github.com/gaitat/GenomeUPlot2184 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 evaluating a...1491 days ago
Nanopolis: polish a genome assembly
...ta. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modu...2172 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...gether. Reducing/removing reference bias as compared to mapping based approaches. The software is designed to work in situations where a whole-genome assembly is not the objective...2171 days ago