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Mapreads is a ABI provided aligner for short length color space reads.

Available on


User documentation

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)
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