Changes between Version 8 and Version 9 of SatelliteSeqAnalysis

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Timestamp:
2009/03/20 16:14:15 (15 years ago)
Author:
bonnalraoul
Comment:

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  • SatelliteSeqAnalysis

    v8 v9  
    1212[http://bowtie-bio.sourceforge.net/index.shtml BOWTIE] Ultra-short reads, Burrows-Wheeler index. [[BR]] 
    1313Lasergene[[BR]] 
    14 GSrapper[[BR]] 
     14[http://www.454.com/products-solutions/analysis-tools/gs-reference-mapper.asp GSMapper] 
     15    *  Map reads to any reference genome and generate a consensus sequence. 
     16    * 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 
     17    * Quickly identify high confidence difference compared to the reference genome, which are singled out in a separate file. 
     18    * Compare large, complex genomes of any size including: resequencing of whole genomes from humans, plants, yeasts, bacteria, fungi, viruses, YACs, BACs, fosmids 
     19    * 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) 
     20[[BR]] 
    1521[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]] 
    1622[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]]