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Old 07-03-2011, 08:24 PM   #7
Location: Ithaca, NY

Join Date: Apr 2010
Posts: 39

Originally Posted by history_of_robots View Post
You are suggesting to use '-a bwtsw'. On BWA manual ( it says: "BWA-SW can also be used to align ~100bp reads, but it is slower than the short-read algorithm." and "On low-error short queries, BWA-SW is slower and less accurate than the first algorithm [IS], but on long queries, it is better". So it is '-a is' that is seemed to be required for BWA indexing a genome for subsequent short read alignment. However, in the same manual page it says: 'IS is moderately fast, but does not work with database larger than 2GB'. A complete genome can be larger than that (for example mm9.fa is 2.5GB). So I am wondering if chromosomes should be indexed separately. Unfortunately, it seems that in this case BWA will have to be run on each chromosome separately it seems. Or is there another way to use IS on the whole genome?
No, what I said is correct - you are thinking of "bwa bwasw" as an alternate to aln + samse/sampe. The -a bwtsw uses the algorithm for indexing a large genome. BWTSW vs. IS has nothing to do with read size - just genome size.
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