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

WBL 26 Nov 2012 (13 July 2017)

If ftp.cs.ucl.ac.uk is too slow please try http://crest.cs.ucl.ac.uk/bowtie2gp

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              

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