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.
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.
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.
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.
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.
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.
A novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. Icarus consists of two major contig viewers: a contig alignment viewer and a contig size viewer.
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.
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.
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.
A graphical interface to contig and trace data in NCBI’s Assembly Archive. The assembly archive was designed to accept two types of data: assembly instructions describing the location and sequence alignment of individual traces within an assembly and assembly alignments describing the alignment of a set of traces to a given assembly.
Aligns finished microbial genomes with the contigs of unfinished genomes. MGView provides a method allowing the generation of several visualizations to facilitate gap closure. It enables visualization of assembly progress for evaluating the extent of contig coverage and the exit point from the random sequencing phase. This tool takes as input a BLAST result report and a nucleotide fasta file of a completed “backbone” genome.