Menu
▾
▴
#8 Iterative trimming in SOAP mode
(From the Bowtie thread on Seqanswers:)
swbarnes2: "Could Bowtie be altered to have an interative trimming function, like SOAP has? I just did a quick comparison, and while untrimmed SOAP and Bowtie had about the same number of aligned reads with no trimming, (and Bowtie was much faster) I find that iteratively trimming the last bases with SOAP, 8 at a time, gives a huge boost to the number of reads that align, up to 30%."
It seems possible to do this pretty well, though perhaps not in exactly the same way as SOAP. Imagine we're reporting 1 hit. The idea would be to keep track of the longest partial alignment found throughout the matching process. If matching fails, then instead of reporting nothing, we report the longest partial alignment. The user might specify a shortest acceptable alignment length and we would use that to determine whether to keep track of a particular partial alignment. More thought is required about whether this would be easy to extend to policies other than the 1-good policy.