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Old 12-05-2013, 12:18 AM   #4
Senior Member
Location: Kuala Lumpur, Malaysia

Join Date: Mar 2008
Posts: 126

Hi Hans,

The options given for Novoalign are all wrong.

If you are using Novoalign with LSC you need to use -r Exhaustive not -r All. This will improve results dramatically and should be better than the other aligners.

For 100bp reads try

novoalign_options = -c1 -r Ex 1000 -t 120 -F FA -g 0 -x 20 -o sam

If read length is different adjust -t accordingly. On Cerebellum reads used by Kin Fai results are 40% better with 30% reduced run time vs BWA using LSC 0.3.1

Best, Colin
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