Difference between revisions of "Karma"

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Ue color space as an example, and say we use NCBI36.fa as 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"
+
{| style="width: 571px; height: 288px" border="1" cellspacing="1" cellpadding="1" width="571"
 
|-
 
|-
 
|  
 
|  
| Base Space  
+
|  
| Color pace
+
Base Space
 +
 
 +
|  
 +
Color Space
 +
 
 
|-
 
|-
| Reference genome
 
| NCBI37-bs.umfa
 
 
|  
 
|  
 +
Reference genome
 +
 +
|
 +
NCBI37-bs.umfa
 +
 
|-
 
|-
| Word Index
 
 
|  
 
|  
NCBI37.umwihi  
+
Word Index
 +
 
 +
|
 +
NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi
  
NCBI37.umwiwp
+
|-
 +
|
 +
Word Hash (Left)
  
 
|  
 
|  
 +
NCBI37-bs.15.5000.umwhl
 +
 
|-
 
|-
| Word Hash (Left)
 
| NCBI37-bs15.umwhl
 
 
|  
 
|  
|-
+
Word Hash (Right)
| Word Hash (Right)  
+
 
| NCBI37-bs15.umwhr  
+
|  
 +
NCBI37-bs.15.5000.umwhr
 +
 
 
|  
 
|  
 
|}
 
|}

Revision as of 13:53, 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 Space

Reference genome

NCBI37-bs.umfa

Word Index

NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi

Word Hash (Left)

NCBI37-bs.15.5000.umwhl

Word Hash (Right)

NCBI37-bs.15.5000.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