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.

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
File format support for ACE, AFG, MAQ, and SOAP, with experimental SAM. Import GFF3 features and quickly find/highlight them.
 * Tablet "lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments"


 * 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?

Current version: ngsview-0.91.tar.gz ???
 * 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)


 * gap5 part of the newest Staden package, it is still a test release? Can accept ACE, MAQ, BAM or BAF formats.