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
- To get started using SHRiMP, read through the the SHRiMP documentation.
How to run SHRiMP
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).