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LANL-Bioinformatics / EDGE

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
https://lanl-bioinformatics.github.io/EDGE/
GNU General Public License v3.0
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bowtie2 alignment mode #25

Closed donutbrew closed 6 years ago

donutbrew commented 6 years ago

I see that for normal reads (not long reads), bowtie2 is set to run in global mode instead of a local mode. This can cause issues in generating consensus sequences in some poorly-trimmed fastq files. I would suggest either to change to use '--local or' '--sensitive-loca'l or to label the bowtie2 button as global alignment (as this may be what you're going for).

chienchi commented 6 years ago

Yes. We use default mode for the aligners. If users would like to turn on specific mode, users can use "Aligner Options" to change the parameters as you suggest here with --local or --sensitive-local. Or, use BWA mem as aligner which will do local alignemnt. Another example is to use "-x ont2d" to run BWA mem with Nanopore reads. And I agree with you that we should put descriptions about the aligners in the documentation site.