| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| readme.txt | 2014-01-27 | 1.1 kB | |
| Makefile | 2014-01-27 | 505 Bytes | |
| util.h | 2013-09-03 | 2.2 kB | |
| util.cpp | 2013-09-03 | 3.6 kB | |
| ReadSimulator.h | 2013-09-03 | 653 Bytes | |
| SeqAssembly.cpp | 2013-09-03 | 11.0 kB | |
| ReadSimulator.cpp | 2013-09-03 | 4.1 kB | |
| Matrix.h | 2013-09-03 | 6.0 kB | |
| Matrix.cpp | 2013-09-03 | 6.9 kB | |
| FastqSimulate.cpp | 2013-09-03 | 525 Bytes | |
| Totals: 10 Items | 36.6 kB | 0 | |
MPSequencing Readme v1.0 Xiaohu Shen xhshen@utexas.edu 1/2014 1 Installation 1.1 Requirements ParticleCall should function on any standard Linux environment with required package Gnu Scientific Library (GSL) (version >= 1.12) 1.2 Compiling instructions From the directory containing the source files, simply type: > make Two runnables are generated: FastqSimulate and SeqAssembly 2 Running instructions After compilation, MPSequencing can be used to randomly generate short read DNA sequencing data file from a genome sequence file in FASTA format. The assemly sequence is obtained using alignment information of the reads to a reference sequence. ex. >./FastqSimulate >./SeqAssembly Output: FastqSimulate generates short reads data file with quality information in FASTQ format. SeqAssembly obtains the reference-guided assembled genome sequence from alignment information and outputs the number of mismatchs between assembled sequence and original sequence. Note: In current implementation the input filenames are hard coded in the file.
