Index of /staff/W.Langdon/ftp/gp-code/bowtie2gp/

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 <int> 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).
      Name                   Last modified     Size  Description              

[UP ] Parent directory [   ] bowtie2-2.2.3gp-align> 24-Aug-14 13:15 11M [   ] bowtie2-align 26-Jul-12 10:53 1.2M [DIR] gp_sources/ 15-Jul-13 19:29 - [DIR] indexes/ 26-Nov-12 16:21 - [   ] README 14-Apr-15 15:56 1K [   ] README~ 14-Apr-15 15:55 1K [BIN] RN_12_09.pdf 21-Jan-13 17:54 492K [GZP] sample1M.out.gz 26-Nov-12 14:44 96M [GZP] sample1M_1.fastq4.gz 15-Nov-12 16:11 34M [GZP] sample1M_2.fastq4.gz 15-Nov-12 16:14 36M
10 files