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...2387 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facili...oring the 3D physical architecture of genomes. Delta takes Hi-C...ng domains and chromatin loops in the genome. It then generates a physical...ool which enhances the integration of genome...2385 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 o...lti-threaded parallelization, allowing to assemble human-sized genomes...2385 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...2329 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 gen...2379 days ago
2379 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...2379 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...1859 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty...Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome...2378 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation o...ntegrate RGM in SPAdes. RGM can be run with other genome assemblers if they use the gr...bsp;From de Bruijn Graphs to Rectangle Graphs for Genome...2377 days ago