Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Techn...ut. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a sp...2089 days ago
2083 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble eac...in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a cl...2083 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-...kb. It has been extensively tested on whole-genome, exon-capture, and ...very large datasets as part of the Thousand Genomes a...2083 days ago
QUAST-LG: Versatile genome assembly evaluation
QUAST-LG-a tool that compares large genomic de novo assemblies against reference seque...nces and computes relevant quality metrics. Since genomes generally cannot be reconstr...uce a concept of upper bound assembly for a given genome and set...2082 days ago
MITOS: improved de novo metazoan mitochondrial genome annotation
Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows...2082 days ago
VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and PDF).2077 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide sy...2077 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succint measure of quality a...eads that map to a site in an assembled genome to calculate a quality score for each position in the genome assembly. We accomplish this...a quality score for every position in a genome assembl...2072 days ago
pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks
pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig bed (many options) bedgraph links (represented as arcs) Hi-C matrices (if HiCExplorer is installed)2067 days ago