Karma

Karma is top secret. Shh!

Download

To get a bootleg copy go to Karma Download

Build Reference

Options

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 structure

Upon successfully building references, you will obtain a list of reference files like below:

	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

Align Illumina Reads

Command line:

karma map -r reference.fa read1.fastq read2.fastq -o output.sam

Align ABI SOLiD Reads

Command line:

karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam

Other useful links

Introduction of BWA usage

Heng Li's thoughts about aligner

Benchmark of Dictionary Structures