mapreads

Summary

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

Available on

Fourierseq

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&nbsp;: reads file (in color space)
ref.fasta&nbsp;: reference genome (in base space)
A=1&nbsp;: count 2 consistent mismatches as 1 mismatch
M=3: allow for 3 mismatches (in seed alone)
L= 35&nbsp;: 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&nbsp;: template file (for 35 length reads with 3 mismatches)