Results for "bacterial"
Bookmarks
shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also su...1210 days ago
Orione – a web-based framework for NGS analysis in microbiology
End-to-end NGS microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the constructi...3565 days ago
Scaffolding of a bacterial genome using MinION nanopore sequencing
Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable wit...3216 days ago
Barrnap: Bacterial ribosomal RNA predictor
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,...2541 days ago
RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline...2921 days ago
- ...er phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes. This readme covers...
2905 days ago
Bioinformatics tools and software
...ures. UCHIME >Chimeric sequence detection. PILER >De novo genome repeat finder. PILER-CR >Detection of CRISPR repeats in bacterial genomes. QSCORE >Comp...2852 days ago
CGView - Circular Genome Viewer
GView is a Java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualizati...2776 days ago
- ...mmand syntax: virmet fetch --viral n, for example, downloads the bacterial database. Other available sub...s so far are fetch download genomes update update viral/bacterial database index index ge...
2755 days ago
Maq: Mapping and Assembly with Quality
...low these steps to try Maq. All you need is a reference sequence file in the FASTA format. Prepare a reference sequence (ref.fasta). Better a bacterial genome. Download maq, maq-da...2712 days ago
