Difference between revisions of "Karma"

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(Align ABI SOLiD Reads: fix argument order)
(Options: prepare for karma 0.9)
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Usage:  
 
Usage:  
  
  karma88 create [options...]
+
Karma expects the sub command to be the first argument on the command lineCurrently, this includes: map, create, header, check and test.
  karma88 map [options...] file1.fastq.gz [file2.fastq.gz]
 
  
Diagnostics:  
+
To align reads, you first create an index:
 +
karma create [options...] somereference.fa
  
  karma88 check [options...]
+
A simple example is:
  karma88 test [options...]
+
  karma create -i phiX.fa
-d -> debug
 
-s [int] -> set random number seed [12345]
 
  
Defaults:  
+
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  ==

Revision as of 17:07, 7 April 2010

Karma is top secret. Shh!

Download

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