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SR-ASM algorithm is designed for DNA assembly of the short 
sequences coming from 454 sequencers. The 454 sequencer 
protocol is based on measuring light intensities generated 
during the sequencing process. The sequences are given as 
nucleotide chains with numbers of their consecutive 
appearances. Additionally to the sequences, one gets rates 
of confidence for every nucleotide. 
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 Configuration
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In config.h there are many parameters. Most significant are:

PROC_NUM - how many processess 

HASH_LENGTH - length of hash

COMPUTATIONAL_TRESHOLD - heuristic threshold which defines when 
pair of sequences should be decline to compare with SW algorithm

SEQUENCE_BEGIN - maximum offset in overlapping sequences


 How to Install
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Unpack file. Type 'make' in directory where program was unpacked.


 How to use
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To use program you need a file with sequences given in fasta 
format and a file with qualities. In the quality file there 
should be given precision for all sequences in format:

>sequence1 name
q1_1 q1_2 q1_3 q1_4 ....
>sequence2 name
q2_1 q2_2 q2_3 q2_4 ....

its very similar to fasta format, but instead of nucleotids 
there are given integer qualities separated by space


To run program type for example:
./alignment.exe sample.fasta sample.qual > results 2>error.log

where
sampla.fasta - file with sequences
sample.qual - file with qualities
results -  file where results should be written to
error.log - file with debug information