Mapreads is a ABI provided aligner for short length color space reads.
How to run mapreads
Example command for running mapreads:
mapreads in.csfasta ref.fasta A=1 M=3 L=35 I=1 S=0 T=/home/scott/coronalite/etc/schemas/schema_35_3 > out
in.csfasta : reads file (in color space)
ref.fasta : reference genome (in base space)
A=1 : count 2 consistent mismatches as 1 mismatch
M=3: allow for 3 mismatches (in seed alone)
L= 35 : length of read
I= 1: reference sequence is multiple sequences.
S= 0: analyze in color space
T= /home/scott/coronalite/etc/schemas/schema_35_3 : template file (for 35 length reads with 3 mismatches)