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.2392 days ago
1442 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific featu...p 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 Sc...2389 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
...he 3D physical architecture of genomes. Delta takes Hi-C...ins and chromatin loops in the genome. It then generates a physical...nts the plausible consensus 3D structure of the genome. Deltaf...ch enhances the integration of genome topology/physical structure with extensive genome annotat...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-b...sets by utilizing lightweight data structures and multi-threaded parall..., allowing to assemble human-sized genomes on commodity clusters in under...2386 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 f...2331 days ago
PASA: Gene Structure Annotation and Analysis
...ym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits...of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with th...2380 days ago
2380 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 bac...ia obtained by differential coverage binning of multiple metagenomes...2380 days ago
snakepipes: A toolkit based on snakemake and python for analysis of NGS data
snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq Hi-C Whole Genome Bi...1861 days ago