Ryan's Blog

Venter Genome Simulation

Posted in Uncategorized by ryanlayer on December 19, 2012

$ wc -ml Simulated_Venter_Chr17.fa
1575757 80363571 Simulated_Venter_Chr17.fa

There are 1575757 lines and 80363571 characters (including new line chars).  Minus new lines, there are 78787814 characters.  The first line is “>Simulated_Venter_Chr17”, which is 24 characters, so the final genome size is 78787790.

To find the number of pairs we want to simulate we use the following formula:

NUM_PAIRS=`echo “($SIZE*$COVERAGE)/($READ_LENGTH*2)” | bc`

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