User talk:Darek Kedra/sandbox 10
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
- 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 reads multiple data files including the standard ACE genome assembly file and optional READS, EGL, and MAP
- SeqMonk seqmonk_v0.7.zip not useful for SNP,
- MapView requires Mono to run on Linux, small memory requirements?
- Integrative Genomics Viewer (IGV) from Broad, java based, oriented more towards clinical data?
- MochiView Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis. ChIP-chip oriented?
- ngsview next-generation sequence alignment editor. Converts (separate scripts) to its native XML format multiple file types (BED, BLAST, Eland, mapview processed MAQ, Corona, ACE and SAM)
Current version: ngsview-0.91.tar.gz ???
- gap5 part of the newest Staden package, it is still a test release? Can accept ACE, MAQ, BAM or BAF formats.