use kanga to align short reads to a reference genome
output files
output files
output log file
process for colorspace (SOLiD)
any extra parameters
print this help and exit
maximum number of intermediate N’s in reads before treating read as unalignable
accept paired end alignments with apparent length of at most this
accept paired end alignments with apparent length of at least this
do not accept multiple reads aligning to the same loci
0 - CSV loci only, 1 - CSV loci + match sequence, 2 - CSV loci + read sequence, 3 - CSV loci + read + match sequence, 4 - UCSC BED, 5 - SAM format
0 - none, 1 - paired ends with recover orphan ends, 2 - paired end no orphan recovery
fastq quality scoring- 0 - sanger, 1m - Illumina 1.3+, 2 - Solexa < 1.3, 3 - Ignore quality
number of processing threads (0 sets threads to number of CPU cores)
trim this number of bases from 3’ end of reads when loading raw reads
trim this number of bases from 5’ end of reads when loading raw reads
print version information and exit