Fine tuning alignments?
Hi all,
I am sequencing a bunch of viral samples (RNA-based <10kb genome) that are fairly divergent from the reference strain (~5-10%). I generally use Mosaik to align the reads (mostly 50bp SE, but we also have 100bp PE) with the following parameters:
-hs 8 -act 14 -mmp 0.10 -m all
Overall it works pretty well, but I have noticed that certain alignment errors are introduced at times (please see image)
If I use Geneious, I can 'Fine tune' the reads and this will correct the errors. However, I would rather not have to use Geneious and would much prefer a more scalable approach. I'm thinking maybe a local realignment tool (e.g. GATK/Picard package) would be the way to go? But I wanted to hear if people had other suggestions? Maybe also try different parameters in Mosaik or a completely different aligner?
Thanks very much in advance.
I am sequencing a bunch of viral samples (RNA-based <10kb genome) that are fairly divergent from the reference strain (~5-10%). I generally use Mosaik to align the reads (mostly 50bp SE, but we also have 100bp PE) with the following parameters:
-hs 8 -act 14 -mmp 0.10 -m all
Overall it works pretty well, but I have noticed that certain alignment errors are introduced at times (please see image)
If I use Geneious, I can 'Fine tune' the reads and this will correct the errors. However, I would rather not have to use Geneious and would much prefer a more scalable approach. I'm thinking maybe a local realignment tool (e.g. GATK/Picard package) would be the way to go? But I wanted to hear if people had other suggestions? Maybe also try different parameters in Mosaik or a completely different aligner?
Thanks very much in advance.