# Default Bowtie command options # because it is in the path: bowtie_command = bowtie # used options: option-a = true option-3 = 5 option-n = 2 option-l = 28 option-y = true option-t = true option--sam = true option-p = 16 option--best = true # Default bowtie build command options bowtie-build_command = bowtie-build # uncomment these options if you wish to use them # buildoption-c = comma-separated list of sequences rather than a list of FASTA files # buildoption-C = true (--color) build a colorspace index # buildoption-a = true (--noauto) disable automatic -p/--bmax/--dcv memory-fitting # buildoption-p = true (--packed) use packed strings internally; slower, uses less mem # buildoption-B = true build both letter- and colorspace indexes # buildoption--bmax = max bucket sz for blockwise suffix-array builder # buildoption--bmaxdivn = max bucket sz as divisor of ref len (default: 4) # buildoption--dcv = diff-cover period for blockwise (default: 1024) # buildoption--nodc = true disable diff-cover (algorithm becomes quadratic) # buildoption-r = true (--noref) don't build .3/.4.ebwt (packed reference) portion # buildoption-3 = true (--justref) just build .3/.4.ebwt (packed reference) portion # buildoption-o = (--offrate) SA is sampled every 2^offRate BWT chars (default: 5) # buildoption-t = (--ftabchars) # of chars consumed in initial lookup (default: 10) # buildoption--ntoa = true convert Ns in reference to As # buildoption--seed = seed for random number generator index_loc = bowtie_index index_basename = Nvitripennis