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 a...parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or im...2081 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
...eletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and ...ta, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, an...2081 days ago
QUAST-LG: Versatile genome assembly evaluation
...gainst reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstr...age regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute...2080 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 allow...2080 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).2075 days ago
Synima: a Synteny imaging tool for annotated genome assemblies
...graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of...2075 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succi...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 assembly. This allows for eas...2070 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)2065 days ago
2065 days ago
Pacasus: Correction of palindromes in long reads from PacBio and Nanopore
Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) confe...2063 days ago