Mapping variable read length

Question

[Chirag Nepal]

Hi There,

Does anyone have a recommendation on tools that allow to map reads of variable length (between 18-300 nt) as can be seen here

https://www.dropbox.com/s/10dn098492zst9i/Length.png?dl=0

I had previously (6 years back) used blat to map such cases, and use percent identity to get mapped reads. Are there some new tools that can efficiently map sequence reads of variable length. thanks !!

Answer 1

[ATpoint]

Any of the popular mapping tools, e.g. bowtie2 or bwa should be able to handle this. What kind of data is this and how certain are you that the small fragments are indeed meaningful and not any noisy byproducts?

Answer 2

[GenoMax]

bbmap.sh from BBMap suite should be able to do this.