Mash: fast genome and metagenome distance estimation using MinHash
Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other...2396 days ago
SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.2394 days ago
1443 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific feat...to produce in silico reads for a given reference genome. NanoSim is written in Python...The source files and manual are available at the Genome Scienc...2390 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facil...ring the 3D physical architecture of genomes. Delta takes Hi-C...g domains and chromatin loops in the genome. It then generates a physical...ol which enhances the integration of genome topolo...2388 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in t...of highly polymorphic (HP) diploid genomes remains challenging. As a re...shortage of tools for assembling HP genomes from the next generation seq...graph assembler, dipSPAdes, for HP genomes that...2388 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...ti-threaded parallelization, allowing to assemble human-sized genomes on co...2388 days ago
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference materi...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 from...2332 days ago
PASA: Gene Structure Annotation and Analysis
PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene s...2382 days ago