SAMSWiki/WebDocumentation/IntroDuction/PreProcessing

The pre-processing part consists in several steps such as:

• cutting low quality parts (usually beginning and end)
• cutting or masking vector and adaptor sequences
• masking repeats
• masking low complexixity regions such as poly A tails
• masking contaminating sequences:
  • bacterial DNA
  • yeast DNA
  • mitochondrial DNA
  • ribosomal DNA

Here are the subsections:

• /QualityClipping
  • /PHRED
  • /Trace2Dbest
• /VectorClipping
  • /VecScreen
  • /XBLAST
• /RepeatMasker
• /Vector and Repeat masking
  • /CrossMatch
  • /Vmatch