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Usage:
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]
debug off (default off) seed 12345 (default 12345)
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 ==
== File structure ==
