Changes between Version 24 and Version 25 of SatelliteSeqAnalysis

Timestamp:

2009/03/24 18:14:50 (16 years ago)

Author:

mn

Comment:

--

SatelliteSeqAnalysis

@@ -8 +8 @@
 
 == Mapping tools ==
-Maq[[BR]]
-ELAND[[BR]]
-[http://bowtie-bio.sourceforge.net/index.shtml BOWTIE] Ultra-short reads, Burrows-Wheeler index. [[BR]]
-[http://www.dnastar.com/ Lasergene] Support 454/Solexa. GUI interface for displaying alignments and contigs organization (scaffolds) [[BR]]
-[http://www.454.com/products-solutions/analysis-tools/gs-reference-mapper.asp GSMapper]
+ * 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
@@ -18 +18 @@
     * 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)
-[[BR]]
-[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. [[BR]]
-[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. [[BR]]
-[http://emboss.sourceforge.net/ EMBOSS]  [[BR]]
+
+ * [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.sourceforge.net/ EMBOSS]
+ * [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] 
+ * [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.
@@ -33 +34 @@
     * 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)
-[[BR]]
-[http://www.dnastar.com/ Lasergene] Support 454/Solexa. GUI interface for displaying alignments and contigs organization (scaffolds) [[BR]]
-[http://www.ebi.ac.uk/~zerbino/velvet/ Velvet][[BR]]
-[http://emboss.sourceforge.net/ EMBOSS] [[BR]]
+
+ * [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.sourceforge.net/ EMBOSS]
 many mores.... but never used.
 
 == Platforms == 
-[http://www.454.com/ Roche, 454] [[BR]]
-[http://www.illumina.com/pages.ilmn?ID=203 Illumina, Solexa] [[BR]]
-[http://www.appliedbiosystems.co.jp/website/jp/home/index.jsp AB, Solid] [[BR]]
+ * [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. [[BR]]
-Some veriations SNP, deletion, insertion can by identified during mapping/assembly process, other things more "new biology" needs more work by bionformaticians.  [[BR]]
-Support from biologists is required in order to discover more new things.
+ * 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. [[BR]]
-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).  [[BR]]
-Editing in real time, providing alternatives for hypothesis. [[BR]]
+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).