User talk:Darek Kedra/sandbox 10

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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


  • 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 not useful for SNP,
  • MapView requires Mono to run on Linux, small memory requirements?

  • 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.

Sequence assembly

Data formats / converters

Software / web sites