WBL 26 Nov 2012 (14 April 2015) Notice Bowtie2 by default looks for the database in directory indexes I have used default (500) for max insert. Bowtie2 command line options: -X or --maxins Default: 500 Optimising Existing Software with Genetic Programming, William B. Langdon and Mark Harman, IEEE Transactions on Evolutionary Computation, Feb 2015, 19(1), 118-135. http://dx.doi.org/doi:10.1109/TEVC.2013.2281544 GECCO 2013 late breaking abstract Which is faster: Bowtie2GP > Bowtie > Bowtie2 > BWA, W. B. Langdon Bowtie2 Manual: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml bowtie2-align --time --seed 9160030 \ h_sapiens_37.5_asm \ -1 sample1M_1.fastq4 \ -2 sample1M_2.fastq4 \ > sample1M.out Contents (decompress with gunzip etc) ~~~~~~~~ bowtie2-align GP improved version of Bowtie2. Linux binary (1.2Mbytes) indexes Bowtie2 format database holding NCBI human genome (release 37 patch 5). 6 files (4Gbytes). sample1M_1.fastq4 Approx 1 million samples from your file IP29_ucl_1.fastq sample1M_2.fastq4 Same as sample1M_1.fastq4 for IP29_ucl_2.fastq (36MB each) sample1M.out Example output file (approx 9 minutes, one 3GHz CPU 1.5 minutes with -p8 and 8 CPUs) (96Mbytes).