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lecture_notes:05-29-2015 [2015/05/29 11:30]
chkan created
lecture_notes:05-29-2015 [2015/05/29 11:37] (current)
chkan Added figures
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 Basic Kmer Counting Basic Kmer Counting
- - Naïve python way [insert picture]+ - Naïve python way (See Figure 1)
  ○ Okay if you're in a microbial genome  ○ Okay if you're in a microbial genome
  ○ Runs out of memory  ○ Runs out of memory
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  ○ Process Kmers one character at a time to avoid building big strings  ○ Process Kmers one character at a time to avoid building big strings
  § Look at sequences a kmer at a time  § Look at sequences a kmer at a time
- ○ How to compress results+ ○ How to compress results ​(See Figure 2)
  § Strings are inefficient way to store kmers  § Strings are inefficient way to store kmers
  § Want to compress keys and values  § Want to compress keys and values
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 </​code>​ </​code>​
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 +Figure 1
 +{{:​lecture_notes:​lecture051915_fig1.jpg?​400|}}
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 +----
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 +Figure 2
 +{{:​lecture_notes:​lecture051915_fig2.jpg?​200|}}
lecture_notes/05-29-2015.1432924233.txt.gz · Last modified: 2015/05/29 11:30 by chkan