From Genome Analysis Wiki
Revision as of 13:53, 24 March 2010 by Zhanxw (talk | contribs)
Jump to navigationJump to search

Karma is top secret. Shh!

  • Download

To get a bootleg copy go to Karma Download

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


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


Word Index

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

Word Hash (Left)


Word Hash (Right)


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