SHRiMP is a an aligner from the University of Toronto which uses a vectored Smith-Waterman for alignment. Although it is slow, it detects alignments with high sensitivity and accuracy. It supports color space data.
Fourierseq - current version: 2.2.1 (updated 11/14/11).
Phylocluster - version: 2.0
SHRiMP (rmapper) results can vary greatly based upon the input parameters. So please select parameters accordingly.
The base commands on Fourierseq are:
for color space:
and for base space:
The input parameters that we typically use with color space data are the following:
gmapper-cs -p opp-in -N 4 -1 F3/V3BC17_RNA.csfasta -2 F5/V3BC17_RNA.csfasta /home/scott/Downloads/mouse.rna.fna > bc17.sam 2> bc17.log &
Tip: To view the actual alignments in base space as part of the output file, add -p option (prettyprint).