Harvest: a suite of core-genome alignment and visualization tools
Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes,...2399 days ago
2399 days ago
Mugsy: multiple whole genome alignment tool
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a cu...strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA fi...: Fast multiple alignment of closely related whole genomes....2399 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes....2387 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in th...of highly polymorphic (HP) diploid genomes remains challenging. As a res...shortage of tools for assembling HP genomes from the next generation sequ...graph assembler, dipSPAdes, for HP genomes...2387 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on...lti-threaded parallelization, allowing to assemble human-sized genomes...2387 days ago
MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes...2331 days ago
Recovery of complete genomes from metagenomes
This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bact...ia obtained by differential coverage binning of multiple metagenomes...2380 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromos...2379 days ago
HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likel...2359 days ago