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mapreads
Summary
Mapreads is a ABI provided aligner for short length color space reads.
Available on
User documentation
- To get started using mapreads, download mapreads manual.
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
where
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)
, multiple selections available,