= Satellite meeting for Sequence analysis tools from the next generation sequencer =

== Topics ==
To share our knowledges about sequence analysis tools.
Please write what you know about the tools. 

Also see [http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html Bioinformatics for Next Generation Sequencing virtual issue] -- yaskaz@ddbj (thanks to ichan) and [http://www.nature.com/nbt/journal/v26/n10/fig_tab/nbt1486_T3.html Table 3 of  Jay Shendure & Hanlee Ji., Next-generation DNA sequencing, Nature Biotech.] (thanks to hinaichigo)

== Mapping tools ==
 * Maq
 * ELAND
 * [http://bowtie-bio.sourceforge.net/index.shtml BOWTIE] Ultra-short reads, Burrows-Wheeler index.
 * [http://www.dnastar.com/ Lasergene] Support 454/Solexa. GUI interface for displaying alignments and contigs organization (scaffolds) 
 * [http://www.454.com/products-solutions/analysis-tools/gs-reference-mapper.asp GSMapper]
    *  Map reads to any reference genome and generate a consensus sequence.
    * Easily view all differences compared to the reference sequence with automatic output to separate files: Insertions (blocks up to 50 bases), Deletions (blocks up to 50 bases), SNPs
    * Quickly identify high confidence difference compared to the reference genome, which are singled out in a separate file.
    * Compare large, complex genomes of any size including: resequencing of whole genomes from humans, plants, yeasts, bacteria, fungi, viruses, YACs, BACs, fosmids
    * Data outputs: fna.file (sequence of contigs, FASTA format), qual.file (corresponding Phred equivalent quality score), ace.file (consensus alignment of the reads against a given reference sequence)

 * [http://compbio.cs.toronto.edu/shrimp/ SHRiMP] supports letter-space (454/Solexa), color-space (Solid) and Helicos 2-pass space. Spaced-seeds followed by S-W. 
 * [http://bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.01.50.html Lastz] Blast(z) variant. Has parameter settings tuned for 454 and Solexa mapping for both reference based assembly and variant discovery. 
 * [http://emboss.open-bio.org/wiki/Next-Generation_Sequencing_Data EMBOSS tools for NGS]
 * [http://last.cbrc.jp/ LAST]
many mores.... but never used.

== Assemble tools ==

 * [http://www.454.com/products-solutions/analysis-tools/gs-de-novo-assembler.asp GSAssembly] 
    *  Performs whole genome shotgun assembly of genomes with or without paired-end data.
    * Order contigs into scaffolds using supported paired-end reads.
    * Assemble larger, more complex genomes up to 400 megabases in size with a 64-bit assembler or up to 20 megabases with a 32-bit assembler.
    * Co-assemble with Sanger Sequencing reads.
    * Select the read files you want to assemble by browsing in the GUI.
    * Data outputs: fna.file (sequence of contigs, FASTA format), qual.file (corresponding Phred equivalent quality score), ace.file (alignment of the reads to contig sequence)

 * [http://www.dnastar.com/ Lasergene] Support 454/Solexa. GUI interface for displaying alignments and contigs organization (scaffolds)
 * [http://www.ebi.ac.uk/~zerbino/velvet/ Velvet]
 * [http://emboss.open-bio.org/wiki/Next-Generation_Sequencing_Data EMBOSS tools for NGS]
many mores.... but never used.

== Platforms == 
 * [http://www.454.com/ Roche, 454]
 * [http://www.illumina.com/pages.ilmn?ID=203 Illumina, Solexa]
 * [http://www.appliedbiosystems.co.jp/website/jp/home/index.jsp AB, Solid]

== Notes ==

 * Every new software must handle this "huge" amount of data. 
 * Some veriations SNP, deletion, insertion can by identified during mapping/assembly process, other things more "new biology" needs more work by bionformaticians.  
 * Support from biologists is required in order to discover more new things.

== TODOs ==

Connected to SatelliteBigData a LIMS infrastructure is suggested for tracking history and infer problems coming from wet-lab. 

From SatelliteVisualization these tools could be very usefull to explore at any level all the informations collected, from the alignment (lower) up to annotation/comparison (higher). The informations are intended as local (faltfile/databases/webservices) or remote (databases/webservices).  

Editing in real time, providing alternatives for hypothesis. 

Easy tools to integrate informations coming from different platforms (illumina, 454, solid).