Unlock your biological data

?

Try: RNA sequencing CRISPR Genomic databases DESeq

1 - 43 of 43 results
filter_list Filters
language Programming Language
build Technology
healing Disease
settings_input_component Operating System
tv Interface
computer Computer Skill
copyright License
1 - 43 of 43 results
IGV / Integrative Genomics Viewer
star_border star_border star_border star_border star_border
star star star star star
(1)
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.
bam.iobio
Offers an overview of the contents of large, non-human-readable BAM files. bam.iobio enables users to investigate their alignments in real time. It can determine information such as: (1) the average read coverage and its distribution, (2) the composition of the data set according to read length, (3) the fragment-length average, distribution and outliers, (4) the histogram of base quality values and read duplication rate, and (5) the histogram of mapping quality values and fraction of properly mapped read pairs.
Geneious
star_border star_border star_border star_border star_border
star star star star star
(1)
Proposes a powerful and comprehensive suite of next generation sequencing (NGS) analysis tools. Through an intuitive and user-friendly interface, Geneious provides visual sequence alignment and editing, sequence assembly, comprehensive molecular cloning and phylogenetic analysis. Users can also simply import and convert a vast range of data types and customize with their own algorithms, plugins or workflows. Furthermore, Geneious increases process efficiency and improves data organisation. This bioinformatics software platform also proposes a high interoperability with good API to link LIMS and other tools. First released in 2005, Geneious is one of the world’s leading bioinformatics software platforms, used by over 2,500 universities and institutes and commercial companies in more than 65 countries.
Highlander
star_border star_border star_border star_border star_border
star star star star star
(1)
Assists users to organize and centralize all variant data and annotations from their lab. Highlander provides researchers several tools for filtering information. This tool, coupled to a local MySQL database, aims to classify all variant data coming from exome- and whole genome sequencing experiments. It also supplies annotations or visualizations functions that allow to detect changes-of-interest amongst the complete list of variants detected in a sample.
IGB / Integrated Genome Browser
An easy-to-use, highly customizable genome browser you can use to view and explore genomic data and annotations, especially RNA-Seq and ChIP-Seq data sets. IGB supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-scale data loading from remote web servers or local files; and dynamic manipulation of quantitative data via genome graphs. We enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation, and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data.
MagicViewer
star_border star_border star_border star_border star_border
star star star star star
(1)
Displays short read mapping and allows identification and annotation of genetic variation based on the reference genome. MagicViewer simplifies the large-scale data interpretation as convenient and effortless as possible in the face of next-generation sequencing (NGS) data. It permits users to modify the appearance of the displayed short read alignment and sequencing depth. This tool furnishes detailed annotation facilities for single nucleotide polymorphisms (SNPs).
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.
CAFE / aCcelerated Alignment-FrEe sequence analysis
Calculates 28 alignment free dissimilarity measures. CAFE allows visualization of pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. It allows the user to study the relationships among genomes and metagenomes. The tool is based on a k-mer alignment-free method and contains 10 conventional measures based on k-mer counts. It also integrates 15 measures based on presence/absence of k-mers.
Bambino
A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs.
ReadXplorer
A freely available comprehensive exploration and evaluation tool for NGS data. ReadXplorer extracts and adds quantity and quality measures to each alignment in order to classify the mapped reads. This classification is then taken into account for the different data views and all supported automatic analysis functions. ReadXplorer is implemented in Java as a Netbeans rich client application. Utilizing a modular programming structure, it enables developers to create their own highly specialized software modules and easily plug them into ReadXplorer.
VOE / Visual Omics Explorer
A cross-platform data visualization portal that is implemented using only HTML and JavaScript code. VOE is a standalone software that can be loaded offline on the web browser from a local copy of the code, or over the internet without any dependency other than distributing the code through a file sharing service. VOE can interactively display genomics, transcriptomics, epigenomics and metagenomics data stored either locally or retrieved from cloud storage services, and runs on both desktop computers and mobile devices.
SeqMonk
star_border star_border star_border star_border star_border
star star star star star
(1)
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.
VING
A standalone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple viewing options, including strand-specific views and a special heatmap mode for representing multiple experiments in a single figure. VING produces high-quality figures for NGS data representation in a genome region of interest. VING input and outputs have been rendered Galaxy-compatible so that automated coverage plots can be easily incorporated in Galaxy pipelines. The resulting, integrated view of a genome region is immediately suitable for figure production.
BasePlayer
Enables tightly integrated comparative variant analysis and visualization of thousands of next generation sequencing (NGS) data samples and millions of variants. BasePlayer is a highly efficient and user-friendly software for biological discovery in large-scale NGS data. It transforms an ordinary desktop computer into a large-scale genomic research platform, enabling also a non-technical user to perform complex comparative variant analyses, population frequency filtering and genome level annotations under intuitive, scalable and highly-responsive user interface to facilitate everyday genetic research as well as the search of novel discoveries.
extractalign
Extracts regions from a sequence alignment. extractalign allows you to specify one or more regions of a sequence alignment to extract sub-sequences from to build up a resulting sub-sequence alignment. This software reads in a sequence alignment and a set of regions of that alignment as specified by pairs of start and end positions (either on the command-line or contained in a file) using gapped alignment positions as the coordinates, and writes out the specified regions of the input sequence in the order in which they have been specified.
trackViewer
Visualizes mapped reads along with annotation as track layers for next generation sequencing (NGS) dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, single nucleotide polymorphisms (SNPs) and methylation data. trackViewer is a package with minimalist design for drawing elegant tracks or lollipop plot. It is minimal designed to plot figure for publication. This tool is based on Gviz but want to draw figures in minimal style for publication. A package that plot data and annotation information along genomic coordinates.
0 - 0 of 0 results
1 - 10 of 10 results
filter_list Filters
computer Job seeker
Disable 2
person Position
thumb_up Fields of Interest
public Country
language Programming Language
1 - 10 of 10 results

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.