npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
...p.npscarf) is a program that scaffolds and completes draft genomes assemblies in...uencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It also facilitates the real-time analysis of po...2600 days ago
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
...lies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of...ASS with existing HTS scaffolders using Illumina paired reads of three bacterial genomes. Our algorithm co...2600 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 bioinformaticians to assemble bacterial genomes sequenced with NextGen...2600 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
...inder is a versatile program to create random shotgun and amplicon s...e libraries based on DNA, RNA or proteic reference sequences provide...nscriptomic, metatranscriptomic, proteomic, metaproteomic shotgun an...e simulated datasets can be used to test the accuracy of bioinformat...2599 days ago
SuRankCo: supervised ranking of contigs in de novo assemblies
...ion sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. https...2599 days ago
AVID: A Global Alignment Program
...ethod, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole...mparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID W...2599 days ago
Synteny Portal: a web-based application portal for synteny block analysis
Synteny Portal, a versatile web-based appl...ructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i...base, (ii) visualize and download syntenic relationships as high-qual...ntuitive and easy-to-use web-based interface. We believe that Synteny...2599 days ago
dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation
...and DataBase for automated Carbohydrate-active enzyme ANnotation...by the BioEnergy Science Center of the DOE. Similar resource...ides the capability of automated and comprehensive CAZyme ann...s; dbCAN provides the most complete set of metagenomic CAZym...2594 days ago
Genome Annotation Transfer Utility (GATU)
...that have already been annotated. For example, whenever a new...GATU, to automatically annotate the new strain using a previo...e reference genome (the annotated strain) to the new sequence...an also be used to help annotate larger genomes (ie. bacterial...2594 days ago
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