ABySS-Explorer Crack For PC (2022)
– Display of a sequence assembly as a directed graph in which nodes represent contigs and edges represent read pair relationships. – Rotated graphs and graphs with colors are supported. – Orientation can be set to radial (top/bottom), cyclic (clockwise/counterclockwise) or free. – ABySS-Explorer Torrent Download performs a graph traversal by allowing the user to expand or contract each contig node in the assembly graph. This traversal also allows the user to obtain contig node information from the ABySS assembly, such as sequence length, coverage and number of paired-end reads. – In addition, the user can select a contig from an ABySS graph to create a new assembly graph that reflects the selection. – Also in accordance with the ABySS assembly, the user can view contig orientation (forward or reverse), and for each contig node, contig sequence, putative contig origin (from which contig was assembled) and contig coverage. – ABySS-Explorer will open automatically using any JAR file that you have in your classpath. Thus, it is unnecessary to change the default Java security policy to allow access to a JAR file before invoking ABySS-Explorer. – ABySS-Explorer is designed to be as intuitive as possible and is very easy to learn and use. – ABySS-Explorer requires JDK 1.7 or later, and you need only Java SE 1.6 or later. Please note: – Graphs are generated using Java. If you are using JDK 1.6 or earlier, the generated graphs will be somewhat different. The old “graph” view can be achieved in the old JDKs by manually specifying the contig orientation, and the old “contig” view can be achieved by deleting all connections. – Under “Help->Question”, please see the front page help for more information about the tool. – Latest updates to the ABySS assembly graph are available from the ABySS website at: ABySS-Explorer is designed with Java. Usage: This is a simple example of a few operations you can perform on the ABySS assembly graphs. First, let us demonstrate the tool’s main features: 1
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ABySS-Explorer is an interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular contig connectivity and supporting paired-end read relationships. Now you can make use of this handy and easy to use sequence assembly viewer. Features: * Interactive graphical display * Graph-based representation of sequence assembly structure * Links between contigs and supporting reads * Filtering by contig or read type * View variant contigs * View mapping reads * Connection graph of contigs and reads * Contig coloring based on assembly length * Real-time updates of contigs and read connections * Command line tool ABySS-Explorer is an interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular contig connectivity and supporting paired-end read relationships. Now you can make use of this handy and easy to use sequence assembly viewer. Features: * Interactive graphical display * Graph-based representation of sequence assembly structure * Links between contigs and supporting reads * Filtering by contig or read type * View variant contigs * View mapping reads * Connection graph of contigs and reads * Contig coloring based on assembly length * Real-time updates of contigs and read connections * Command line tool ABySS-Explorer is an interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular contig connectivity and supporting paired-end read relationships. Now you can make use of this handy and easy to use sequence assembly viewer. Features: * Interactive graphical display * Graph-based representation of sequence assembly structure * Links between contigs and supporting reads * Filtering by contig or read type * View variant contigs * View mapping reads * Connection graph of contigs and reads * Contig coloring based on assembly length * Real-time updates of contigs and read connections * Command line tool ABy 2f7fe94e24
ABySS-Explorer Crack Serial Key [Win/Mac] (Updated 2022)
Introduction ABySS-Explorer is a Java application that uses a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular contig connectivity and supporting paired-end read relationships. Aim ABySS-Explorer’s aims are to give a simple (but rich) interface to explore assembly structure, identify contig overlaps, detect assembly errors, quickly examine contig names, and find alignment and paired-end read relationships. Features Graph-based Representation ABySS-Explorer uses a graph-based representation to display the assembly graph. Eulerian Paths ABySS-Explorer uses Eulerian paths (i.e. paths that start and finish at the same vertex) to represent edges. The edges form the vertices of the graph. All vertices are labelled by contigs and original sequence reads. Edges can be labelled by up to three contigs and up to four original sequence reads. Edges can be directed or undirected. Edges can be set to have a fixed length, a fixed weight, or randomly assigned a length and weight. Eulerian paths are indicated by red arrows. Read Nodes ABySS-Explorer has read nodes for any original sequence reads in the assembly graph. Nodes are coloured by chromosome and depth of coverage. Read Nodes can be placed anywhere in the graph (i.e. not just on vertices) and the colour of the read node indicates its chromosome and depth of coverage. Edges connecting read nodes to contigs (i.e. contig nodes) can be set to have a fixed length or randomly assigned a length and weight. Contig Nodes Contig nodes are coloured by length. Contig nodes can be placed anywhere in the graph. Contig nodes can be labelled. Contig nodes can be visually connected by placing read nodes between them. Contig connections can be directed or undirected. Contig nodes can be joined by an edge, which can be set to have a fixed length or randomly assigned a length and weight. Read Nodes Read nodes can be placed anywhere in the assembly graph (i.e. not just on vertices) and labelled by read ID. Read nodes
What’s New in the ABySS-Explorer?
ABySS is a metagenomics assembler for de novo assembly of very large datasets. An interactive Java application, ABySS-Explorer, has been written to serve a different but equally demanding purpose: i) Explore the structure of an ABySS assembly and the connectivity relationships it creates between contigs. ii) Inspect read pair information from paired-end sequence data. Package Overview: ABySS-Explorer is a Java application developed using the Java Eclipse SDK (version 2.1) and the Rich Faces MVC framework (version 2.0.2). It has been tested against Java 1.4 and 1.5, and the Rich Faces framework is required to utilize the “mvc:annotation-driven” spring bean in order to make use of the annotations provided by ABySS. Key Features: – Graphical user interface (GUI) – Sequence assembly and meta data is displayed graphically using a novel custom representation – Paired-end sequence data is displayed visually, allowing users to confirm the correct orientation and distance relationship of the reads. – Three different views are available – A simple tree view that shows assembled contigs and their connectivity between one another. – A graph view that shows the read pairs and their supporting contigs. – A cytogenetic view that visualizes the spatial distribution of contigs along the reference genome. – Read orientation can be inferred from pair orientation. – Meta data such as read lengths and positions is displayed. – Read quality information is displayed in the form of an average phred score by read. – ABySS metagenomics assembly information is displayed as well. – Optionally the program can report back assembly statistics such as length, size, number and class of contigs, N50 value, total number of bases, number and percent of paired-end reads. Usage: – Double click on the “ABySS Explorer” icon on the Eclipse start up screen to start the application – Connections between contigs are shown by the edges of the contigs. – Contigs are represented by colored nodes (red for contigs and yellow for connections). – Contigs are connected to one another by edges. – Read pairs are shown as lines. – Pairing of reads is determined by which ends of the read have an edge connecting them to one another. – The program calculates and displays these relationships automatically. – Nucleotide
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