2014-01-30

pipeline 5.0.3

--local (required) - end trimming

-M 100 (remove)

-N 0 (required) - 0 mismatches to seed

-L 20 (modify) - specifies seed length - should be set to 1/2 minimum alignment length since we're requiring 100% identity

-i S,1,0 (modify) - need to reduce the number of seeds tested - to test every 5 seeds from a 300mer, the combo would be S,1,0.23

--mp 1000,1000 (reqired) - all scoring options seem OK for a minimum alignment length of 50

--np 1000

--rdg 1000,1000

--rfg 1000,1000

--score-min L,100,0

--no-mixed (remove)

--fr (required)

--no-discordant (required)

--ignore-quals (required)

count reads with alignment > 50bp