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Aug 20 '18 at 14:28 answer Bioathlete timeline score: 4
Aug 20 '18 at 9:59 comment added terdon @Bioathlete you may as well post that as an answer so the question isn't left hanging.
Aug 20 '18 at 9:36 comment added Matt Bashton I have successfully used BWA and Bowtie2 for this sort of task, you may want to explore various parameters and how they affect the overall alignment rate.
Aug 20 '18 at 7:00 comment added Cedric Stroobandt @Bioathlete: No, I haven't tried it yet because BWA and BOWTIE2 were indeed designed for "whole genomes" while my reference is extremely small. I wondered if there were any methods that were commonly used in that case. Maybe not, and BWA or BOWTIE might still be the optimal choice, even for a small reference. That's as good an answer as any. I'll wait a little longer for extra suggestions, otherwise I'll consider the question answered. Thanks!
Aug 19 '18 at 15:36 comment added Bioathlete Have you tried using whole genome aligners like BWA and BOWTIE2 with your custom reference? These are designed for NGS input and alignment of larger numbers or reads against a single reference.
Aug 19 '18 at 11:56 comment added Cedric Stroobandt @Llopis: yes, it is known which reads belong to the same mutant. I haven't used multi sequence alignment because I don't want to align all sequences to eachother, as I'm only interested in differences with the reference. As for time: at this moment it's still manageable to use common local alignment algorithms like Smith-Waterman, but if there's an approach that's just faster than this, it will help in the scale-up to even more high-throughput.
Aug 19 '18 at 10:48 comment added llrs Have you tried using some multi sequence alignments tools like T-coffe, or clustal? How many time are you willing to spend/how much accuracy do you want? Do you know which reads belong to each single mutant or is all in a pool?
Aug 19 '18 at 8:55 review First posts
Aug 19 '18 at 15:36
Aug 19 '18 at 8:51 history asked Cedric Stroobandt CC BY-SA 4.0