SeqMonk is a Java application for visualising and analysing mapped sequence data.
It’s designed for high throughput sequencing experiments and works with datasets that can be represented as genomic positions, letting users explore aligned reads against annotated genomes and carry out downstream quantitative and statistical analysis within the same program.
This is free and open source software.
Key Features
- Imports mapped sequence data from formats such as BAM, SAM, and Bowtie.
- Creates data groups to support visualisation and comparative analysis workflows.
- Quantitates mapped data flexibly so different datasets can be compared.
- Performs statistical analyses to identify regions of interest.
- Generates reports containing both experimental data and genome annotation.
- Some functionality can make use of a local R installation.
Website: www.bioinformatics.babraham.ac.uk/projects/seqmonk/
Support:
Developer: Babraham Bioinformatics / Simon Andrews
License: GNU General Public License v3.0
SeqMonk is written in Java. Learn Java with our recommended free books and free tutorials.
Related Software
| Desktop Genome Browsers | |
|---|---|
| IGV | High-performance visualization genome browser tool |
| IGB | Integrated Genome Browser |
| JBrowse | Fast, scalable genome browser |
| Tablet | Graphical viewer for sequence assemblies and alignments |
| UGENE | Set of integrated bioinformatics software |
| Artemis | Genome viewer and annotation tool |
| Apollo | Instantaneous, collaborative genomic annotation editor |
| CutePeaks | Cross platform Sanger Trace file viewer |
| Genome Workbench | Integrated tools for studying and analyzing genetic data |
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