CLA: Contig-Layout-Authenticator
...ut-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, result...l genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated...2552 days ago
A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
...d for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly again...2544 days ago
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SuRankCo: supervised ranking of contigs in de novo assemblies
SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes...2533 days ago
Omega2: metagenome assembly pipeline
...transitive edges 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...2486 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
...genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and.... A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented usin...2366 days ago
ONT assembly and Illumina polishing pipeline
...ing steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina dataset onto the contigs obtained in the previous step...2349 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...t for high-coverage bacterial genomes, it is possible to generate long contigs from raw PacBio or ONT reads...$2"\n"$3}' reads.gfa | fold > reads.fa And then count how many contigs: grep ">" reads.fa | wc...2346 days ago
Opera: An optimal genome scaffolding program
...y program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequen...2345 days ago