GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
...m, which combines contig order, distance and orientation in a single optimization objective. The resulting optimization problem is solved using an expectation-maximization procedure...2599 days ago
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
...nformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be fr...2599 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
...rrent sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or...2598 days ago
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 conti...2598 days ago
AVID: A Global Alignment Program
...nic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative compari...and methods should be useful for future studies. The tools we have developed for the alignment comparison...2598 days ago
Synteny Portal: a web-based application portal for synteny block analysis
...eny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignme...ill serve as a highly valuable tool that will enable biologists to easily perform comparative genomics stu...2598 days ago
Genome Annotation Transfer Utility (GATU)
...sing BLAST, VGO and BBB. Afterwards, they can either be accepted for/rejected from annotation. GATU can handle multiple-exon genes as well as mature peptides. Although it was design...2593 days ago
2593 days ago
NovelSeq: Novel Sequence Insertion Detection
The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. http://novelseq.sourceforge.net/Home Paper at https://www.ncbi.nlm.nih.gov/pubmed/203857262582 days ago
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads htt...and much more.GraphMap is also used as an overlapper in a new de novo genome asse...correction, for which a highly sensitive overlapper is required.Currently, devel...2584 days ago