Changes

= Overview =

= Overview =

KARMA(K-tuple Alignment with Rapid Matching Algorithm) is able to map 35bp single end color space reads at the speed of approximately <math>1.2-2.0 \times 10^9</math> reads per hour using Intel Xeon X760 2.66GHz and 128G memory.

KARMA (K-tuple Alignment with Rapid Matching Algorithm) is able to map 35 bp single end color space reads at the speed of approximately <math>1.2-2.0 \times 10^9</math> reads per hour using Intel Xeon X760 2.66GHz and 128G memory.

We summarize software requirments as following:

We summarize software requirements as following:

*&nbsp; Binary reference genome in nucleotide space (see [[#Input_file_requirement|Input file requirement]]})  

*&nbsp; Binary reference genome in nucleotide space (see [[#Input_file_requirement|Input file requirement]]})  

*&nbsp; Specify color space parameter when starting KARMA (see [[#Map_Color_Space_Reads|Map Color Space Reads]])<br>  

*&nbsp; Specify color space parameter when starting KARMA (see [[#Map_Color_Space_Reads|Map Color Space Reads]])<br>  

Please note the hardwares requirment for KARMA are:

Please note the hardware requirements for KARMA are:

*20G memory. Due to memory share mechanism, running multiple processes of KARMA on the same machine consumes about the same amount of memory asrunning one process.<br>  

*20G memory. By using shared memory for the word index tables, multiple instances of KARMA can run on one machine yet consume about the same amount of memory as running one process.<br>  

*30G disk space  

*30G disk space  

<br> We listed a complete example reviewing the whole procedure from building word index to mapping color space reads in [[#A_Complete_Example|A Complete Example]].

<br> We show a complete example reviewing the whole procedure from building word index to mapping color space reads in [[#A_Complete_Example|A Complete Example]].

= Build Binary Reference Genome and Word Index<br> =

= Build Binary Reference Genome and Word Index<br> =