2100 days ago
BASE: a practical de novo assembler for large genomes using long NGS reads
new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads...o generate adaptive seeds that have high probability to appear uniquely in the genome....2085 days ago
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 Technol...tput. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome...2085 days ago
2080 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 each...on in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome...2080 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
...s up to several kb. It has been extensively tested on whole-genome, exon-capture, and ...has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinic...2079 days ago
QUAST-LG: Versatile genome assembly evaluation
QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstr...duce a concept of upper bound assembly for a given genome...2079 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 al...2078 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).2074 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-...2074 days ago