User talk:Darek Kedra/sandbox 10: Difference between revisions
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==Visualization of mappings== | ==Visualization of mappings== | ||
* [http://bioinf.scri.ac.uk/tablet/ Tablet] "lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments" | * [http://bioinf.scri.ac.uk/tablet/ Tablet] "lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments" | ||
File format support for ACE, AFG, MAQ, and SOAP, with experimental SAM. | |||
Import GFF3 features and quickly find/highlight them. | |||
* [EagleView http://bioinformatics.bc.edu/marthlab/EagleView] reads multiple data files including the standard ACE genome assembly file and optional READS, EGL, and MAP | |||
==Sequence assembly== | ==Sequence assembly== | ||
Revision as of 13:45, 10 December 2009
Next Gen Seq software / ideas
Solexa reads quality
- SHREC 2009 Java program, rudimentary web site, includes test data, input as fasta with ACTG only.
Short reads mapping
Spliced
- ERANGE ERANGE3.1.tgz, which was released on 2009/04/17.
- [ http://www.genoscope.cns.fr/externe/gmorse/ G-Mo.R-Se]
- TopHat is a fast splice junction mapper for RNA-Seq reads
- FLUX CAPACITOR "focuses on abundancy prediction for splice forms, transcripts and alternative splicing events from reads generated by applying new sequencing technologies"
Visualization of mappings
- Tablet "lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments"
File format support for ACE, AFG, MAQ, and SOAP, with experimental SAM. Import GFF3 features and quickly find/highlight them.
- [EagleView http://bioinformatics.bc.edu/marthlab/EagleView] reads multiple data files including the standard ACE genome assembly file and optional READS, EGL, and MAP
