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AliTV—interactive visualization of whole genome comparisons
By Jit 3194 days agogithub.com - AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are...assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference...
By Jit 3039 days agohttp://assemblytics.com/ - Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip...NanoPack: visualizing and processing long-read sequencing data
By Jit 2982 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...Hawkeye: an interactive visual analytics tool for genome assemblies
By Abhimanyu Singh 2838 days agoamos.sourceforge.net - Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Jit 2450 days agogithub.com - MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome...
Tools for Geospatial data analysis !
Last updated 1297 days ago by BioStarGeospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools can help you work with data from a variety of sources, including satellite imagery, GPS data,...GFinisher: a new strategy to refine and finish bacterial genome assemblies
By Jit 2997 days agogfinisher.sourceforge.net - 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 the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2240 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...RAMI: a tool for identification and characterization of phylogenetic clusters in microbial...
By Jit 3350 days agoacademic.oup.com - RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly. Availability: RAMI is licensed...Translational Bioinformatics: Transforming 300 Billion Points of Data
By Jitendra Narayan 4798 days agoTranslational Bioinformatics: Transforming 300 Billion Points of Data into Diagnostics, Therapeutics, and New Insights into Disease Air date: Wednesday, June 20, 2012, 3:00:00 PM Time displayed is Eastern Time, Washington DC Local...
