Read alignment visualization software tools | High-throughput sequencing data analysis
The rapid growth of next-generation sequencing (NGS) technologies has led to a wide variety of short read DNA datasets. Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data.
Conducts next generation sequencing (NGS) investigation. Geneious provides visual sequence alignment and editing, sequence assembly, comprehensive molecular cloning and phylogenetic analysis. It increases process efficiency and improves data organization. This tool enables the importation and conversion of a vast range of data types and offers a solution to customize researchers’ algorithms.
Enables users to explore large, integrated genomic datasets. IGV provides next-generation sequencing (NGS) data visualization and provides features for identification of sequencing and analysis artifacts, leading to errant single-nucleotide variant (SNV) calls, as well as support for viewing large-scale structural variants (SV) detected by paired-end read technology. The software also includes features to support third-generation long-read sequencing technologies. Several IGV features have been developed to aid manual review of aligned reads.
A program to enable the visualisation and analysis of mapped sequence data. SeqMonk was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions. It's main features are: (i) Import of mapped data from mapped data (BAM/SAM/bowtie etc), (ii) Creation of data groups for visualisation and analysis, (iii) Visualisation of mapped regions against an annotated genom, (iv) Flexible quantitation of the mapped data to allow comparisons between data sets, (v) Statistical analysis of data to find regions of interest and (vi) Creation of reports containing data and genome annotation.
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.
Offers an intuitive user interface and built-in workflows for a variety of genomic applications that guide researchers though every step of the analysis process. Partek Genomics Suite gives biologists, bioinformaticists, and statisticians a single, integrated solution for trustworthy results with a user-friendly interface, comprehensive workflows, and ability to support all next generation sequencing, microarray, and qPCR platforms.
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 free tool for displaying pairwise comparisons between two or more DNA sequences. ACT can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.