Results for "Genome"
Tags
Scripts for the analysis of HGT in genome sequence data.
Scripts for the analysis of HGT in genome sequence dataTags: scripts, analysis, HGT, genome, sequence, data
2333 days ago
Bandage: interactive visualization of de novo genome assemblies
Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequ...Tags: Bandage, interactive, visualization, de novo, genome, assemblies
2328 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, whic...Tags: COPE, accurate, k-mer, pair-end, reads, connection, tool, genome, assembly
2327 days ago
jobTree based python wrapper to run the genome simulation tool suite Evolver
evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also...Tags: jobTree, python, wrapper, genome, simulation, tool, suite, Evolver
2324 days ago
- Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to To...
Tags: kSNP3.0, SNP, detection, phylogenetic, analysis, genomes, alignment, reference, genome
2324 days ago
Mugsy: multiple whole genome alignment tool
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FA...Tags: Mugsy, multiple, whole, genome, alignment, tool
2324 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation (if you have only a few genomes to annotate). Pr...Tags: Tools, bacterial, whole, genome, annotation, prokaryotic, genes
2316 days ago
Mash: fast genome and metagenome distance estimation using MinHash
Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is available in and GCC >= 4.8 and OSX >= 10....Tags: Mash, fast, genome, metagenome, distance, estimation, MinHash
2320 days ago
String graph based genome assembly software and tools !
In graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication. In recent Genome Research paper describing an...Tags: String, graph, genome, assembly, software, tools !
2313 days ago
