CLA: Contig-Layout-Authenticator
...tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds. Script https://sourcef...2557 days ago
2541 days ago
npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing clust...2539 days ago
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
...ared GRASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes. Our algorithm constructs a comparable number of scaffolds, but makes fewer errors. This...2539 days ago
Omega2: metagenome assembly pipeline
...dges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using mate-pair information....2491 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
...a stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. In...2371 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...e based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial a...2355 days ago
Opera: An optimal genome scaffolding program
...ees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y.Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-e...2350 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
...-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless other...2319 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig S...2258 days ago