Karma

Karma is top secret. Shh!

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To get a bootleg copy go to Karma Download

Build Reference

Options

Command line

Usage:

Karma expects the sub command to be the first argument on the command line. Currently, this includes: map, create, header, check and test.

To align reads, you first create an index:

karma create [options...] somereference.fa

A simple example is:

karma create -i phiX.fa

To actually align reads, use the map command:

karma map [options...] mate1.fastq.gz [mate2.fastq.gz]

A simple example is:

karma map -r phiX.fa -o phiX.sam mate1.fastq.gz mate2.fastq.gz

To facilitate SAM RG values being set automatically in a production environment, we keep a header in the reference. The header can be viewed and edited using the header subcommand:

karma header -r phiX.fa

Due to the size and complexity of Karma input, output and index files, various checks and tests are useful, so we include some diagnostics capabilities:

Tests for external files:

karma check [options...] file.bam file.fastq file.sam file.fa file.umfa

Tests internal to Karma:

karma test [options...]
-d -> debug
-s [int] -> set random number seed [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 -o output.sam read1.fastq read2.fastq

Align ABI SOLiD Reads

Command line:

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

Other useful links

Introduction of BWA usage

Heng Li's thoughts about aligner

Benchmark of Dictionary Structures