454: Extremely general question

[Protaeus]

All,

I have 454 and PacBio SRA data (that are cleaned of adaptors) that I'd like to align to a reference. I've tried bwasw, but when I look at the alignments in samtools tview, they are rather subpar as compared to data that has been reported by others on these sequences. Any suggestions for general approaches to aligning long reads? bwasw should work, correct? Better tools for dealing with these data?

[ulz_peter]

I guess it depends on how many reads you've got. For a moderate number of seuqences BLAT does a good job as well.
I used bwasw for 454 data as well and it worked out nicely.

[RCJK]

How about Newbler for the 454 reads? Not sure how it would deal w/ PacBio data, but if you use fasta + qual I think it could handle it (depending on read length).