i have now single-end solexa data and later will be also working on PE.
i've tried soap2 for the -g 5 option for gapped alignment, however, on known indels, there's nothing properly mapped. although i've seen on seqanswers someone did gapped alignment successfully (but on soap rather than soap2?). and the developer says soap2 can do gapped PET alignment, but "gapped" means the interval between the ends rather than indels?
bowtie says it doesn't support gapped alignment yet.
may anyone tell me which free software can do gapped alignment (for indels) on both SE and PE data? many thx!
i've tried soap2 for the -g 5 option for gapped alignment, however, on known indels, there's nothing properly mapped. although i've seen on seqanswers someone did gapped alignment successfully (but on soap rather than soap2?). and the developer says soap2 can do gapped PET alignment, but "gapped" means the interval between the ends rather than indels?
bowtie says it doesn't support gapped alignment yet.
may anyone tell me which free software can do gapped alignment (for indels) on both SE and PE data? many thx!
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