Karma
Karma is top secret. Shh!
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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
