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Karma uses an existing reference to align short reads, such as generated by Illumina sequencers.
Karma uses an existing reference to align short reads, such as generated by Illumina sequencers.
The current version, 0.9.0, is optimized to rapidly map base space reads from Illumina sequencers. This version does not map color space reads, nor does it reliably map LS454 reads. Both of those features will return in Karma 0.9.1.
The current version, 0.9.0, is optimized to rapidly map base space reads from Illumina sequencers.
Color space and LS454 sequence alignments are not working. These features will return in Karma 0.9.1.
= Download Karma =
= Download Karma =
Karma works using a set of index and hash files created from an existing reference. Once created, this set of reference index and hash files must always be specified in the command line when aligning reads.
Karma works using a set of index and hash files created from an existing reference. Once created, this set of reference index and hash files must always be specified in the command line when aligning reads.
In concept, the simplest workflow is to first create a reference index using 'karma create', then align reads using 'karma map'. You only have to build the index and hash once.
In concept, the simplest workflow is to first create a reference index using ''karma create'', then align reads using ''karma map''. You only have to build the index and hash once.
Because the reference can be large, and because Karma will share the reference among many running instances of Karma, it is useful to put well known references in a common location readily accessible to you and your collaborators.
Because the reference can be large, and because Karma will share the reference among many running instances of Karma, it is useful to put well known references in a common location readily accessible to you and your collaborators.
= Build Reference =
= Build reference index and hash =
Building a reference with Karma is straightforward, but because it is time consuming for longer genomes, you typically save the reference index between runs.
Building a reference index and hash with Karma is straightforward, but because it is time consuming for longer genomes, you typically save the reference index between runs.
The simplest example for creating a reference and index using a wordsize of 11-mer words is:
The simplest example for creating a reference and index using a wordsize of 11-mer words is:
= Aligning Reads =
Aligning reads to the reference is easy:
karma map -r phiX.fa -w 11 phiX.fastq
or for paired reads:
karma map -r phiX.fa -w 11 phiX-mate1.fastq phiX-mate2.fastq
In both of the above examples, the -r option names the reference originally used to build the index/hash, and the -w 11 specifies that we are using the index/hash built for 11-mer words. Although you can use the default word size of 15 for phiX, the index is 4^15 * 4 = 4GBytes, so a shorter word size is prudent.
== Aligning Reads (Illumina) ==
Karma is set up so that the default options work well for mapping Illumina reads to the Human genome.
== Aligning Reads (ABI SOLiD) ==
Karma has been designed to align color space reads. However, in Karma 0.9.0, this functionality is not working.
== Aligning Reads (LS 454) ==
Karma has been designed to align LS 454 reads. However, in Karma 0.9.0, this functionality is not working.
== Options ==
== Options ==
