QSRA - Quality Value Guided Short Read Assembler

QSRA requires a UNIX machine with at least 4GB of RAM. More RAM may be necessary depending on the size of the input data.

Invoke QSRA as follows:
qsra
-f <A single fasta file containing all the sequence reads (*.fa file)> (REQD)
-k <Integer, length of read contained in -f file, min=20> (REQD)
-q <A single Q-values file containing the Q-values of the reads in the fasta file in exactly the same order as they appear in the fasta file> (Optional)
-m <Integer, minimum sufficient Q-value to use when extending contig based on Q-value> (Optional, only used when -q is set. Default=20, min=-40)
-o <Integer, minimum contig size to print to output file.> (Optional, default=parameter specified as -k)
-u <Integer, standard minimum overlap> (Optional, default=18, min=12)
-l <Integer, lower minimum overlap> (Optional, default=16, min=12, max=(-u) parameter)
-t <Integer, minimum number of votes necessary to extend contig (before optional Q-values condition is exercised)> (Optional, default=5, min=1)
-v <Integer, maximum number of disagreements with majority base> (Optional, default=4, min=1)
-c <Float, ratio of most represented base required for extension, default=0.60, min=0, max=1)
-r <0 or 1, specifies whether to output suspected repeated regions to an additional file.> (Default 0)
-x <Integer, maximum number of votes accepted when extending contig> (Optional, required if printing suspected repeated regions. Default=infinite, recommended=10-20x expected coverage)