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Mapreads is a ABI provided aligner for short length color space reads.
edit Available on
Fourierseq
edit User documentation
- To get started using mapreads, download mapreads manual.
edit 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
| Code Block |
|---|
in.csfasta : reads file (in color space) |
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ref.fasta : reference genome (in base space) |
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A=1 : count 2 consistent mismatches as 1 mismatch |
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M=3: allow for 3 mismatches (in seed alone) |
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L= 35 : length of read |
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I= 1: reference sequence is multiple sequences. |
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S= 0: analyze in color space |
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T= /home/scott/coronalite/etc/schemas/schema_35_3 : template file (for 35 length reads with 3 mismatches) |