| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| s_4_0013_int.txt | 2012-08-10 | 320.7 MB | |
| s_4_0080_int.txt | 2012-08-10 | 330.2 MB | |
| Readme.txt | 2012-08-10 | 3.1 kB | |
| SOVA_supervised.c | 2012-08-10 | 100.4 kB | |
| FB_supervised.c | 2012-08-10 | 103.1 kB | |
| FB.c | 2012-08-10 | 99.0 kB | |
| SOVA.c | 2012-08-10 | 96.3 kB | |
| Totals: 7 Items | 651.3 MB | 0 |
// Guidelines to run FB and SOVA // //FB// Compile FB.c using the following command: gcc FB.c -o FB -L/usr/lib -llapack -lblas -I/usr/include/atlas Notes: You must have LAPACK and BLAS in /usr/lib and ATLAS in /usr/include. Change the paths to these if necessary. Running FB Use the command : ./FB source_file1 destination_file1 source_file2 destination_file2 .... eg. ./FB /home/local/altair/phix174_76cycle/s_4_0080_int.txt /home/local/altair/Dynamic/s_4_0080.fastq source_file1 must be an Illumina intensity .txt file. Make sure the path is specified. destination file1 is the output .fastq for source_file1. //SOVA// Compile SOVA.c using the following command: gcc SOVA.c -o SOVA -L/usr/lib -llapack -lblas -I/usr/include/atlas Notes: You must have LAPACK and BLAS in /usr/lib and ATLAS in /usr/include. Change the paths to these if necessary. Running SOVA Use the command : ./SOVA source_file1 destination_file1 source_file2 destination_file2 .... eg. ./SOVA /home/local/altair/phix174_76cycle/s_4_0080_int.txt /home/local/altair/Dynamic/s_4_0080.fastq source_file1 must be an Illumina intensity .txt file. Make sure the path is specified. destination file1 is the output .fastq for source_file1. //FB_supervised// Compile FB_supervised.c using the following command: gcc FB_supervised.c -o FB_supervised -L/usr/lib -llapack -lblas -I/usr/include/atlas Notes: You must have LAPACK and BLAS in /usr/lib and ATLAS in /usr/include. Change the paths to these if necessary. Running FB_supervised Use the command : ./FB source_file1 destination_file1 source_file1_Bus source_file2 destination_file2 source_file2_Bus.... eg. ./FB_supervised /home/local/altair/phix174_76cycle/s_4_0080_int.txt /home/local/altair/Dynamic/s_4_0080.fastq /home/local/altair/Dynamic/s_4_0080_seq.txt source_file1 must be an Illumina intensity .txt file. Make sure the path is specified. destination file1 is the output .fastq for source_file1. source_file1_Bus must be a Illumina sequence file. Also change gen_size to the appropriate size of the genome and the paths to the genome sequence and its reverse complement in the Supervised_alignment function. //SOVA_supervised// Compile SOVA_supervised.c using the following command: gcc SOVA_supervised.c -o SOVA_supervised -L/usr/lib -llapack -lblas -I/usr/include/atlas Notes: You must have LAPACK and BLAS in /usr/lib and ATLAS in /usr/include. Change the paths to these if necessary. Running SOVA_supervised Use the command : ./FB source_file1 destination_file1 source_file1_Bus source_file2 destination_file2 source_file2_Bus.... eg. ./SOVA_supervised /home/local/altair/phix174_76cycle/s_4_0080_int.txt /home/local/altair/Dynamic/s_4_0080.fastq /home/local/altair/Dynamic/s_4_0080_seq.txt source_file1 must be an Illumina intensity .txt file. Make sure the path is specified. destination file1 is the output .fastq for source_file1. source_file1_Bus must be a Illumina sequence file. Also change gen_size to the appropriate size of the genome and the paths to the genome sequence and its reverse complement in the Supervised_alignment function.
