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→Overview
= Overview =
= Overview =
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.
KARMA (K-tuple Alignment with Rapid Matching Algorithm) is able to map 35 bp single end color space reads at a 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 requirements as following:
We summarize the input data requirements as following:
* Binary reference genome in nucleotide space (see [[#Input_file_requirement|Input file requirement]]})
* A binary conversion of the genome reference sequence as nucleotides (see [[#Build_Binary_Reference_Genome_and_Word_Index|Build Binary Reference Genome and Word Index]]})
* Binary reference genome and word index in color space (see [[#Build_Binary_Reference_Genome_and_Word_Index|Build Binary Reference Genome and Word Index]])
* A binary conversion of the genome reference sequence as colors plus word indices in color space (see [[#Build_Binary_Reference_Genome_and_Word_Index|Build Binary Reference Genome and Word Index]])
* Color space reads in valid color space FASTQ format (see [[#Input_file_requirement|Input file requirement]] for file specification)
* Color space reads in color space FASTQ format (see [[#Input_file_requirement|Input file requirement]] for a description)
* Color space reads are longer than minimum length requirement. (see [[#Minimum_read_length_requirement|Minimum read length requirement]])
* Color space reads longer than a minimum length requirement. (see [[#Minimum_read_length_requirement|Minimum read length requirement]])
* Specify color space parameter when starting KARMA (see [[#Map_Color_Space_Reads|Map Color Space Reads]])<br>
* Specify color space parameter when starting KARMA (see [[#Map_Color_Space_Reads|Map Color Space Reads]])<br>
*30G disk space
*30G disk space
<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]].
<br> We show a complete example demonstrating the whole procedure from building the 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> =
