Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Ci...s using long sequencing reads", Hunt et al, Genome Biology...2243 days ago
2243 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic...s by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to valida...2237 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). I...2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Ho...2235 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to...amples of the various output types, see the CGView gallery. http://wishart.biology....2207 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTM...nomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any...2198 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotid...ssification using targeted short read sequencing.” Source Code for Biology...2157 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It...s/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is d...2086 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multipl...2146 days ago
CBS Comparative Microbial Genomics group - BioTools download page
he CMG-biotools system presents a stand-alone interface for comparative microbial g...ough the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the...2144 days ago