A technical report about “Homopolymer Length Filters” is available here.
Miller et al. (2008) and Au et al. (2012) used “compression” for some applications (thanks to Ruibang Luo and Steven Salzberg for pointing these out). Here we discuss general filters, general applications, and general properties of the filters.
“Earplugs”, a wrapper which adds basic filters to existing read alignment software, will be available on this website.
For more information about “Earplugs” or the fast permutations-based aligner for long reads, please contact us.