Difference between revisions of "Karma"

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Karma is top secret. Shh!
+
Karma is top secret. Shh!  
  
* Download
+
*Download
  
To get a bootleg copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]
+
To get a bootleg copy go to [http://www.sph.umich.edu/csg/pha/karma/download/ Karma Download]  
  
* Command line
+
*Command line
 
+
<pre>Usage:
<pre>
 
Usage:
 
 
   karma88 create [options...]
 
   karma88 create [options...]
 
   karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
 
   karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
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   karma88 check [options...]
 
   karma88 check [options...]
 
   karma88 test [options...]
 
   karma88 test [options...]
   -d -> debug
+
   -d -&gt; debug
   -s [int] -> set random number seed [12345]
+
   -s [int] -&gt; set random number seed [12345]
  
 
Defaults:
 
Defaults:
Line 23: Line 21:
  
 
</pre>
 
</pre>
 +
*File strucutre
 +
 +
Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).
 +
 +
Ue color space as an example, and say we use NCBI36.fa as reference genome:
 +
 +
{| style="width: 445px; height: 150px" border="1" cellspacing="1" cellpadding="1" width="445"
 +
|-
 +
|
 +
| Base Space
 +
| Color pace
 +
|-
 +
| Reference genome
 +
| NCBI37-bs.umfa
 +
|
 +
|-
 +
| Word Index
 +
|
 +
NCBI37.umwihi
  
* File strucutre
+
NCBI37.umwiwp
  
Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).
+
|
 +
|-
 +
| Word Hash (Left)  
 +
| NCBI37-bs15.umwhl
 +
|
 +
|-
 +
| Word Hash (Right)
 +
| NCBI37-bs15.umwhr
 +
|
 +
|}
  
Ue color space as an example, and say we use NCBI36.fa as reference genome:
+
<br>
  
  basespace.umfa    => NCBI36.bs.umfa
+
  basespace.umfa    =&gt; NCBI36.bs.umfa
  colorspace.umfa    => NCBI36.cs.umfa
+
  colorspace.umfa    =&gt; NCBI36.cs.umfa
  colorspace.umwhr    => NCBI36.cs.12.umwhr
+
  colorspace.umwhr    =&gt; NCBI36.cs.12.umwhr
  colorspace.umwhl    => NCBI36.cs.12.umwhl
+
  colorspace.umwhl    =&gt; NCBI36.cs.12.umwhl
  colorspace.umwihi    => NCBI36.cs.12.umwihi
+
  colorspace.umwihi    =&gt; NCBI36.cs.12.umwihi
  colorspace.umwiwp    => NCBI36.cs.12.umwiwp
+
  colorspace.umwiwp    =&gt; NCBI36.cs.12.umwiwp
  
* Other useful links:
+
*Other useful links:
  
[http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf Introduction of BWA usage]
+
[http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf Introduction of BWA usage]  
  
[http://lh3lh3.users.sourceforge.net/bioinfo.shtml Heng Li's thoughts about aligner]
+
[http://lh3lh3.users.sourceforge.net/bioinfo.shtml Heng Li's thoughts about aligner]  
  
 
[http://lh3lh3.users.sourceforge.net/udb.shtml Benchmark of Dictionary Structures]
 
[http://lh3lh3.users.sourceforge.net/udb.shtml Benchmark of Dictionary Structures]

Revision as of 09:07, 24 March 2010

Karma is top secret. Shh!

  • Download

To get a bootleg copy go to Karma Download

  • Command line
Usage:
   karma88 create [options...]
   karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
Diagnostics:
   karma88 check [options...]
   karma88 test [options...]
   -d -> debug
   -s [int] -> set random number seed [12345]

Defaults:

debug off (default off)
seed 12345 (default 12345)

  • File strucutre

Color space mapping needs 6 files, and base space mapping needs 5 files (only need to use 1 reference genome).

Ue color space as an example, and say we use NCBI36.fa as reference genome:

Base Space Color pace
Reference genome NCBI37-bs.umfa
Word Index

NCBI37.umwihi

NCBI37.umwiwp

Word Hash (Left) NCBI37-bs15.umwhl
Word Hash (Right) NCBI37-bs15.umwhr


basespace.umfa    => NCBI36.bs.umfa
colorspace.umfa    => NCBI36.cs.umfa
colorspace.umwhr    => NCBI36.cs.12.umwhr
colorspace.umwhl    => NCBI36.cs.12.umwhl
colorspace.umwihi    => NCBI36.cs.12.umwihi
colorspace.umwiwp    => NCBI36.cs.12.umwiwp
  • Other useful links:

Introduction of BWA usage

Heng Li's thoughts about aligner

Benchmark of Dictionary Structures