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Consed
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.
Tablet
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.
EagleView
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.
Hawkeye
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.
Bandage / Bioinformatics Application for Navigating De novo Assembly Graphs Easily
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.
TGNet / Transcript to Genome Consistency Network
Generates tables for visualization in Cytoscape from FASTA sequence and scaffolding information files. TGNet contains scripts that evaluates genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. This approach allows systematic evaluation of genome assemblies’ quality, and thus could be useful for large-scale sequencing projects such as the i5K initiative.
DNPTrapper
An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. DNPTrapper differs from previous tools by providing flexibility and an overview that greatly simplifies the finishing process, by allowing the user to view whole repeat regions at once and to edit assembly errors manually by drag and drop. The program implements and visualizes the results of a previously described statistical method that detects defined nucleotide positions (DNPs, representing single base differences between repeat units) in the presence of sequencing errors.
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