We are interested din the following feature and wondering if it is provided by bowtie2?
To review, the idea would be to have multiple, independently indexed files (bug1.fnt -> bug1.bt2, bug2.fnt -> bug2.bt2) and do something like bowtie2 -x bug*.bt2.
This could be useful for larger genomes (e.g. human). One could have each chromosome indexed separately and then only map against the chromosomes of interest.
Last edit: Gholamali Rahnavard 2014-07-21