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Home modified by Benjamin Lee

Benjamin Lee — Sat, 11 Jan 2014 21:24:12 -0000

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 This program was written while working in the Department of Physics and Astronomy at Johns Hopkins University.  I would like to thank Dr. Richard Wilton for all of his guidance.

 [[project_admins ]] 
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WikiPage Home modified by Benjamin Lee

Benjamin Lee — Mon, 08 Oct 2012 19:54:15 -0000

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Mon, 08 Oct 2012 19:53:46 -0000

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 Modern high-throughput DNA sequencers typically generate short DNA sequences of about 100 bases in length.  Because a 100-base DNA sequence is relatively short, a commonly-used technique for dealing with longer DNA sequences is to use biochemical manipulations to generate much longer sequences of predetermined length and then to sequence the 100 bases at each end.  The DNA sequencer records these "paired-end reads" in two files in which paired reads are located in corresponding positions in each file.
 
 This "paired file comparison" program compares two such files to validate that they do indeed contain paired-end reads.  It compares the metadata of the sequences at corresponding positions in each file.  Because both files are validated from start to end, the program ensures that the files correspond to each other and that no data have been inserted or deleted.  This process of validating metadata also serves as a reasonable test of data integrity in general, as any data corruption that affects the metadata will be detected.
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+Please note that the majority of the documentation for the code appears to the right of the code itself.                                  
 
 
 
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  appears to the right of the code itself.         //like so

- +

Acknowledgments:

+This program was written while working in the Department of Physics and Astronomy at Johns Hopkins University. I would like to thank Dr. Richard Wilton for all of his guidance. [[project_admins ]]

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Mon, 01 Oct 2012 00:53:32 -0000

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+By Benjamin C.G. Lee
+
 Summary:

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Sat, 29 Sep 2012 18:04:05 -0000

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 Summary:
 
 
-Modern high-throughput DNA sequencers typically generate short DNA sequences of about 100 bases.  A commonly-used technique for dealing with longer DNA sequences is to use biochemical manipulations to generate much longer sequences of predetermined length and then to sequence the 100 bases at each end.  The DNA sequencer records these "paired-end reads" in two parallel files in which paired reads are located in corresponding positions in each file.
+Modern high-throughput DNA sequencers typically generate short DNA sequences of about 100 bases in length.  Because a 100-base DNA sequence is relatively short, a commonly-used technique for dealing with longer DNA sequences is to use biochemical manipulations to generate much longer sequences of predetermined length and then to sequence the 100 bases at each end.  The DNA sequencer records these "paired-end reads" in two files in which paired reads are located in corresponding positions in each file.
 
-This "paired file comparison" program compares two such files to validate that they do indeed contain paired-end reads.  It compares the metadata of the sequences at corresponding positions in the files.  Because both files are read and compared from start to end, the program ensures that the files do indeed correspond to each other and that no data have been inserted or deleted.  This process of validating read metadata also serves as a reasonable validation of data integrity in general, as any corruption of the data in the file that affects the metadata will be detected.
+This "paired file comparison" program compares two such files to validate that they do indeed contain paired-end reads.  It compares the metadata of the sequences at corresponding positions in each file.  Because both files are validated from start to end, the program ensures that the files correspond to each other and that no data have been inserted or deleted.  This process of validating metadata also serves as a reasonable test of data integrity in general, as any data corruption that affects the metadata will be detected.
 
 
 
@@ -36,7 +36,7 @@
 
 Performance:
   
-On a CPU with multiple cores, performance tends to be limited by disk I/O bandwidth.  For example, the first time the program is run using two specific files after the computer has been turned on will take much longer than subsequent runs.
+On a CPU with multiple cores, performance tends to be limited by disk I/O bandwidth.  When running on 8 concurrent threads with a 3GHz CPU, the program requires 8 seconds to validate two 4.06 GB FASTQ files each containing 26.5 million reads. 
 
 
 Sample Files:

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Wed, 19 Sep 2012 01:29:17 -0000

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 This "paired file comparison" program compares two such files to validate that they do indeed contain paired-end reads.  It compares the metadata of the sequences at corresponding positions in the files.  Because both files are read and compared from start to end, the program ensures that the files do indeed correspond to each other and that no data have been inserted or deleted.  This process of validating read metadata also serves as a reasonable validation of data integrity in general, as any corruption of the data in the file that affects the metadata will be detected.
 
 
+
 System requirements:  
 
  - Operating Systems:
   -- Windows 7
   -- Linux
 
- 
-- Memory:
 
 
 Command-line syntax:

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Tue, 18 Sep 2012 01:17:12 -0000

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  Additional Notes:
-
  The majority of the documentation for the code 
  appears to the right of the code itself.         //like so 
+
+
 
 
 [[project_admins ]]

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Tue, 18 Sep 2012 01:07:09 -0000

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   -- Windows 7
   -- Linux
 
-
- - Memory:
+ 
+- Memory:
 
 
 Command-line syntax:

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Tue, 18 Sep 2012 01:06:57 -0000

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  - Operating Systems:
   -- Windows 7
   -- Linux
+
 
  - Memory:

WikiPage Home modified by Benjamin Lee

Benjamin Lee — Tue, 18 Sep 2012 01:06:45 -0000

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 System requirements:  
 
  - Operating Systems:
-   - Windows 7
-   - Linux
+  -- Windows 7
+  -- Linux
 
  - Memory: