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...s on the high accuracy of Illumina sequence by eschewing an explicit er..., allowing to assemble human-sized genomes on commodity clusters in under...2388 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...2333 days ago
PASA: Gene Structure Annotation and Analysis
...Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene...with the most recently available experimental sequence data. PASA also identifies an...2382 days ago
2382 days ago
Recovery of complete genomes from metagenomes
...pts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacter...obtained by differential coverage binning of multiple metagenomes Mads Albertsen, Philip H...2382 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 B...1863 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 I...2381 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 A...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 u...2380 days ago
GPOPSIM: a simulation tool for whole-genome genetic data
GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome s...2361 days ago