lecture_notes:04-27-2011
Differences
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lecture_notes:04-27-2011 [2011/05/02 10:54] eyliaw created |
lecture_notes:04-27-2011 [2011/05/02 11:00] 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 | ||
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| * <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.txt · Last modified: 2011/05/02 11:00 by eyliaw
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