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 O...ord Nanopore sequencing. The pipeline can run on a computing cluster as w...s of positional information such as gene ordering and the detection of ge...2598 days ago
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-genera...g assemblies capable of using diverse information sources. GRASS...lation of the contig scaffolding problem, which combines contig o...d binary quadratic programming approximation of the original prob...2598 days ago
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformatici...with NextGeneration Sequencing (NGS) platforms quickly, easily and effecti...2598 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grind...shotgun and amplicon datasets from current sequencing technolo...sed to help decide between alternative sequencing methods for...2597 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 s...ins with alignments of contigs with known reference genomes and predicts...ps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0644...2597 days ago
AVID: A Global Alignment Program
...ethod is designed to be fast, memory efficient, and practical for sequence alignment...regions up to megabases long. We present numerous applications of.../mouse alignments. We have also performed a quantitative comparis...publicly available. See Web Site References section for AVID Web...2597 days ago
Synteny Portal: a web-based application portal for synteny block analysis
Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Sy...ng multiple species by using prebuilt alignments in the UCSC...l. http://bioinfo.konkuk.ac.kr/synteny_portal/2597 days ago
dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation
dbCAN is a web server and DataBase for automated Carbohydrate-active enzyme A... CAT. All data in dbCAN are generated based on the famil...en genome submitted by the user; dbCAN provides an explicitl...N make all pre-computed data freely available to the public,...2592 days ago
Genome Annotation Transfer Utility (GATU)
Genome Annotation Transfer Utility (GATU) was designed t...efficient annotation of similar genomes using genomes that have already been annotated. For example, whenever a new strai...sing a previously-annotated strain of SARS CoV. This saves re...uo;s genes in a single step. ORFs present in the target genom...2592 days ago
2592 days ago