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 NextGe...2533 days ago
Genome Annotation Transfer Utility (GATU)
...enes as well as mature peptides. Although it was designed for use with viral genomes, GATU can also be used to help annotate larger genomes (ie. bacterial genomes). The output is save...2527 days ago
DarkHorse: a method for genome-wide prediction of horizontal gene transfer
...ction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic exa...2503 days ago
DIYA: a bacterial annotation pipeline for any genomics lab
DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV http://gmod.org/wiki/Diya2495 days ago
Unicycler: Hybrid assembly pipeline for bacterial genomes
Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only...2362 days ago
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
...ackground annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, wit...2358 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...hes with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or...2349 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...a dozen of PacBio and Oxford Nanopore (ONT) bacterial data sets. Including the mapp...step, it takes about 3 minutes to assemble a bacterial genome. Under the default set...asm confirms that at least for high-coverage bacterial genomes, it is possible to ge...2345 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
...using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The metho...2155 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes t...2104 days ago