SeqMonk
| Function | A tool to visualise and analyse high throughput mapped sequence data |
|---|---|
| Language | Java |
| Requirements | A suitable Java Runtime Environment |
| Code Maturity | Stable. This code is being widely used for real work, although SeqMonk is still under active development. |
| Code Released | Yes, under GPL v3 or later. |
| Initial Contact | Simon Andrews |
Download Now |
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SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It 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:
- Import of mapped data from mapped data (BAM/SAM/bowtie/maq etc)
- Creation of data groups for visualisation and analysis
- Visualisation of mapped regions against an annotated genome.
- Flexible quantitation of the mapped data to allow comparisons between data sets
- Statistical analysis of data to find regions of interest
- Creation of reports containing data and genome annotation
Documentation
A copy of the SeqMonk documentation is available for you to try before you buy (well download..).
You can also look at the material for our SeqMonk training course which might provide a better introduction if you're using the program for the first time. Or the material for our advanced SeqMonk course for a more in depth look at how to apply SeqMonk to your data.
Changelog
- 22-02-13: Version 0.24.1 released
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- Fixed a bug in RNA quantitation for unmerged transcripts
- Fixed a bug causing MACS user options to not be read
- Fixed a crash in the visible store parser
- Fixed an axis label layout bug in the probe trend plot
- Fixed a crash in the intensity difference filter when run with a very small list of probes
- 11-02-13: Version 0.24.0 released
-
- Added GFF export option to reports
- Added antisense transcription pipeline
- Added automatic feedback to crash reports
- Added an ID field to reports
- Added a probe length quantitation
- Added a smoothing subtraction quantitation
- Added a probe name filter
- Added the ability to do gene level RNA-Seq quantitation
- Added a Chi-Square contingency test statistical filter
- Added a raw count option to the RNA-Seq pipeline
- Added the ability to specify the order of highlighted sublists in the scatterplot
- 11-12-12: Version 0.23.1 released
-
- Fixed a bug causing crashing from invalid chromosome names in imported data
- Allowed per-chromosome normalisation in the cis/trans quantitation
- Added per-chromsome filtering to the cis/trans scatterplot
- Added an option to export valid interaction ends into a probe list to the HiC heatmaps
- 3-12-12: Version 0.23.0 released
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- Many improvements in existing HiC tools performance
- Improved HiC statistics - thanks to Robert Sugar and Bori Gerle from Nick Luscombe's group
- Added a MACS style peak caller
- Added splicing efficiency quantitation pipeline
- Added name based probe filtering
- Windowed filters can now group by features
- Added sublist colouring to the scatterplot
- Added customisable colour gradients to all gradient views
- Allow quantitations to be viewed as bars, lines or points
- Allow filtering by mapping quality when importing BAM/SAM
- 6-9-12: Version 0.22.0 released
-
- Major revision to all HiC tools - read the release notes!
- New HiC statistical model
- More controls on HiC heatmap creation
- Improved HiC import filters
- HiC cis:trans scatterplot
- Eigenvector quantitation method to detect chromatin domains
- New 4C enrichment quantitation method
- New consecutive probe generator
- Windowed filters can now use consecutive probes
- Added feature name filter
- Improved deduplication filter
- 17-4-12: Version 0.21.0 released
-
- Added full tracking to all filters
- Added Monte-Carlo statistics filter
- Added bisulphite quantitation pipeline
- Added Hierarchical clustering tool
- Added HiC cis/trans quantitation method
- Made Scatter/MA plots interactive
- Added option to make multiple 4C datasets easily
- Improved HiC heatmaps and associated tools
- Fixed bug in HiC import for data with warnings
- Fixed SVG corruption bug
- Fixed Boxwhisker scaling display bug
- 24-1-12: Version 0.20.0 released
-
- Fixed a bug which corrupted filtered probe lists in probe sets containing multiple probes at exactly the same position - see release notes for details
- Fixed a bug which caused the Intensity Difference Filter to add the same hit multiple times
- Fixed a bug in the deduplicated view of HiC data
- Added a quantitation pipeline for wiggle type plots
- 3-1-12: Version 0.19.0 released
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- Greatly improved load and save speed
- Greatly reduced memory profile
- Higher read densities in the chromosome view
- More colour options in the chromsome view
- Improved aligned probes plot
- 22-11-11: Version 0.18.0 released
-
- Added RNA-Seq Quantitation pipeline
- Improved loading speed on multi-CPU machines
- Added HiC probe matrix view
- Improved controls for HiC plots
- Added SeqMonk reimport parser to pass data between projects
- Fixed MA Plot label positions
- Fixed distance filtering in HiC plots
- Fixed windows launcher for non-english locales
- Fixed generic text import on gzipped files
- 27-09-11: Version 0.17.1 released
-
- Fixed a launcher bug for OSX systems with more than 10GB RAM
- Fixed a bug when creating HiC heatmaps with more than 44k probes
- Added an option to send HiC coordinates back to the chromosome view
- Added a fixed value quantitation method
- 22-09-11: Version 0.17.0 released
-
- Added support for HiC read data
- Added a native windows exe launcher
- Launchers now auto-configure memory settings
- Added support for very large annotation sets
- Added a Z-score transformation option to the quantitation tools
- Added a match distribution option to the quantitation tools
- Added a new statistical filter for pairwise comparison of samples without replicates
- Added an MA plot view
- Allow data import to be cancelled
- Allow annotation import for multiple files in a single operation
- Added support for gzipped files in all data import filters
- Added a preview panel when browsing for projects to open
- Changed (again!) the way log transformed empty probes are handled
- 17-06-11: Version 0.16.0 released
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- Added a launch script for linux so you don't have to write out your own launch command
- Added a work round to allow importing paired end tophat files
- Added an option to save feature search results as an annotation track
- Manual correlation filter can now correlate against up to 12 profiles simulataneously
- Percentile normalisation quantitation can use a probe list to calculate the normalisation factor
- The probe trend plot can now operate over the currently visible region of the chromsome view
- 20-05-11: Version 0.15.0 released
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- Allow import of introns from spliced BAM/SAM files
- New probe generator to make probes over every different read position
- New probe generator to merge and deduplicate an existing probe set
- New quantitation method to count exact overlaps between reads and probes
- Feature import from GFFv3 and GTF files
- Changed the way empty probes are handled during quantitation
- Allow zooming within histograms
- New trend plot options to weight all probes equally in the final plot
- 15-03-11: Version 0.14.1 released
-
- Fixed an import bug for paired end data in BAM/SAM format. If you use these please read the release notes
- Fixed a minor import bug in paired end bowtie files
- Improved the smoothing of trend plots
- Added an option to put running window probes inside an existing probe set
- Added an option to reverse all reads in a data set
- 08-02-11: Version 0.14.0 released
-
- Added a cumulative distribution plot
- Added a percentile normalisation quantitation method
- Added a scale to the genome view
- Allow the import of multiple annotation files in the same operation
- Fixed a load of bugs (see release notes)
- 13-01-11: Version 0.13.1 released
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- Added a correlation matrix display
- Added proper scales to all figures and graphs
- Fixed a number of important bugs (see release notes)
- 29-11-10: Version 0.13.0 released
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- Data can now be imported from BAM files
- Quantitations can be exported in BedGraph format
- New line graph display for examining trends over multiple data stores
- New clustering and correlation tools for identifying groups with similar quantitation profiles
- Added a per-probe normalisation quantitation method
- 30-09-10: Version 0.12.0 released
-
- Added a whole genome quantitated data view
- Fixed a genome update bug when only a single track was in the chromosome view
- Fixed a crash in the Replicate Set editor
- 13-09-10: Version 0.11.0 released
-
- Fixed importing SAM files containing unmapped reads
- Can now import bismark files which split up CHH and CHG methylation context
- Biological replicates can now be grouped into replicate sets
- Added a statistical filter for biological replicates
- Added an aligned probe view to look at individual probe trends
- Allow plotting of multiple probe lists in a boxwhisker plot
- 24-08-10: Version 0.10.2 released
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- Fixed many bugs including:
- Spliced reads can now be imported without splitting and will span the proposed splice junction
- You can now extend reads and remove duplicates when using the generic text import
- Saving a project can now be cancelled safely
- Reports can now be cancelled and restarted correctly
- The cache indicator now shows when the cache is actually being used
- Many feauture mapping operations should be much quicker
- 28-06-10: Version 0.10.1 released
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- Fixed a bug which removed drawing optimisation in the chromsome viewer
- Fixed a bug which caused the genome viewer to list negative positions
- Enabled some new layout options for packed read data
- 25-06-10: Version 0.10.0 released
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- Made probes directional and added new visualisation and quantitation which uses this
- More support for removing or ignoring duplicate reads
- Option to extend single end reads to make analysing ChIP-Seq data easier
- Generic text import for features
- Added a genome annotation update mechanism
- New quantitation methods - enrichment quantitation and manual correction
- Import of bisulphite seq data mapped with bismark
- Improved speed when loading / saving projects
- 14-04-10: Version 0.9.1 released
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- Fixed a bug in help when installed in a directory containing a space
- Fixed the ProbeList Probe Generator which was broken
- Check whether data is quantitated before launching views which require this
- Speed up switching between probe lists
- Add more validation to user supplied probe lists
- 09-03-10: Version 0.9 released
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- ProbeLists are now heirarchical so you can follow how they were created
- Offical support for importing additional annotation
- Disk caching now caches annotation as well as reads
- Added an interstitial probe generator
- Added a probe length histogram
- 21-01-10: Version 0.8 released
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- Added a disk cache mode to handle really big datasets
- Added a DataStore summary report
- Added a base pair quantitation
- Fixed the SAM parser to correctly assign strand information
- Updated and improved training course manual
- 05-11-09: Version 0.7 released
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- Fixed a bug when reassembling DataGroups when DataSets have repeated names
- Added a Feature based report
- Added a Scatterplot
- 02-09-09: Version 0.6.1 released
-
- Fixed a bug in generic text import
- Fixed a bug in chromosome name translation
- 01-09-09: Version 0.6 released
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- Import from Maq and SAM files, including support for spliced reads
- Added a Probe Trend view
- Added a Probe length filter
- Made help searchable
- Many speed improvements
- 23-07-09: Version 0.5.2 released
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- Fixed problems with data import (especially GFF)
- Added Probe value distribution filter
- Added ProbeSet from ProbeList generator
- 26-06-09: Version 0.5 released
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- Improved memory management
- Clearer colour scheme
- Auto scaling after quantitation
- Now saves all display preferences
- New relative quantitation method
- Recently used file list
- Automatic check for new releases
- 29-04-09: Version 0.4 released
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- Many optimisations to improve speed
- Automated Error Reporting
- Added Bowtie import filter
- 26-02-09: Version 0.3 released
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- Allow negative values in the data track
- Added coverage depth quantitation
- Allow importing probes from a file
- Added a BoxWhisker plot and a corresponding outlier filter
- Added a toolbar for common tasks
- Added SVG export of all figures
- Improved help files and reader
- Added an Eland import filter
- Many optimisations to reduce memory usage and speed up the display
- 16-09-08: Version 0.2 released
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- Import from GFF and BED files
- Allow multiple file import
- Better handling of data groups
- More efficient handling of large data sets
- Added probe value histogram
- Added option to show just probes or reads
- 30-10-07: Version 0.1 released
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- Initial release
- All basic functions working