Difference between revisions of "Karma"

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(Align Illumina Reads: fix argument order)
(Align ABI SOLiD Reads: fix argument order)
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karma map -r reference.fa -c read1.fastq read2.fastq -o output.sam
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karma map -r reference.fa -c -o output.sam read1.fastq read2.fastq
 
</pre>
 
</pre>
 
  
 
= Other useful links =
 
= Other useful links =

Revision as of 16:54, 7 April 2010

Karma is top secret. Shh!

Download

To get a bootleg copy go to Karma Download

Build Reference

Options

Command line

Usage:

  karma88 create [options...]
karma88 map [options...] file1.fastq.gz [file2.fastq.gz]

Diagnostics:

  karma88 check [options...]
karma88 test [options...]
-d -> debug
-s [int] -> set random number seed [12345]

Defaults:

debug off (default off) seed 12345 (default 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