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lecture_notes:04-27-2011

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lecture_notes:04-27-2011 [2011/05/02 03:54]
eyliaw created
lecture_notes:04-27-2011 [2011/05/02 04:00] (current)
eyliaw
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   * 37 gb per run (~28 gb of raw images)   * 37 gb per run (~28 gb of raw images)
 ===== Software ===== ===== Software =====
-  * Amplicon ​variant analyzer +  * Amplicon ​Variant Analyzer: for specific region analysis 
-  * GS Assembler+  * GS Assembler: de Novo or Reference Mapper
   * GS Reporter   * GS Reporter
   * GS RunProcessor - Image/​signal processing   * GS RunProcessor - Image/​signal processing
Line 51: Line 51:
     * <40 bases, throws sequence away.     * <40 bases, throws sequence away.
     * (Even unfiltered, quality scores will reflect low quality areas)     * (Even unfiltered, quality scores will reflect low quality areas)
 +  * SFFtools can also perform screen-trimming with a screening db for known contaminants.
 A good run: expect a read length mode ~500 and mean >​300. ​ ~50% should pass filters. A good run: expect a read length mode ~500 and mean >​300. ​ ~50% should pass filters.
 +===== de Novo Assembly =====
 +  * All assemblers use .sff files.
 +  * 3, 8 & 20kb paired end libraries.
 +  * Can accept fasta/qual reads.
 +  * 15-25X coverage best.
 +    * Low coverage: poor contig building
 +    * High coverage: may cause contig breaks
 +  * 4 bytes per __read__ base in RAM.
  
lecture_notes/04-27-2011.1304333646.txt.gz · Last modified: 2011/05/02 03:54 by eyliaw