Karma

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	NCBI37-cs.umfa
Word Index	NCBI37-bs.15.5000.umwiwp NCBI37-bs.15.5000.umwihi	NCBI37-cs.15.5000.umwiwp NCBI37-cs.15.5000.umwihi
Word Hash (Left)	NCBI37-bs.15.5000.umwhl	NCBI37-cs.15.5000.umwhl
Word Hash (Right)	NCBI37-bs.15.5000.umwhr	NCBI37-cs.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