Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to tr...reads are corrected using the short reads. Current approaches rely on various graph based alignment techniques an...2082 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 region in parallel. BAUM can: (1) perform reference-...2016 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).2011 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKES...1996 days ago
1996 days ago
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
NovoGraph: building whole genome graphs from long-read-based de novo assemblies An a...thmically novel approach to construct a genome graph representation of long-read-b...vide a proof of principle by creating a genome graph of seven ethnically-diverse h...1995 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the cluste...ve links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to inte...1968 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses....experiments. Because of its activating role, if we overlap the genes that are bound by H...association. Similary, we can perform such kind of overl...1952 days ago
1938 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
...r the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, an...y Heng Li. Contigs are assembled for every 25kb window (with some small overlap) for every region in the ge...1927 days ago