Assembly visualization software tools | De novo genome sequencing data analysis
One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short subsequences produced by current technologies. The final stages of the genome assembly process inevitably require manual inspection of data inconsistencies and could be greatly aided by visualization.
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). The package also covers most of the standard sequence analysis tasks such as restriction site searching, translation, pattern searching, comparison, gene finding, and secondary structure prediction, and provides powerful tools for DNA sequence determination.
A program for viewing and editing assemblies prepared by the Phrap assembly program. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads.
A lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine.
A tool for visualising assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colours and extracting sequences. BLAST searches can be performed within the Bandage GUI and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analysing de novo assemblies that are not possible through investigation of contigs alone.
Provides a visualization tool for large-scale assembly data. Hawkeye intends to increase sequence quality by assisting in detection and correction of assembly errors thanks to a combination of interactive visualization and computational predictors. The software allows users to visualize data and ranking components with three different viewing modes. It can be used for investigating assemblies of all sizes and is compatible with a wide range of assemblers, such as Phrap, Celera Assembler or ARACHNE. Hawkeye is a part of the AMOS toolkit.
Provides assistance for the visualization of data generated by Pacific Biosciences Sequencing Systems. SMRT View allows users to explore and interact with multiple types of analysis results such as resequencing, de novo, cDNA and barcoding. This software offers multiple options to visualize base modifications, base identification and motifs analysis results. It is based on an open source genome browser and is platform-independent.
An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation.