SOAP2.18 (short oligonucleotide analysis package) is a versatile and fast aligner for short reads. It uses the 2-way burrows-wheeler transform to reduce the amount of memory needed while mapping. It handles only base space data.
Because SOAP does not handle color space data, the only way to use SOAP with color space reads is to convert both the reads and the reference to mock base space.
Example pipeline for running soap with color space reads (when dealing with base space reads, follow step 3 onwards)
1. Convert the reference to mock base space.
bs2cs ref.fasta > ref.csfasta
cs2mbs ref.csfasta > ref.m.fasta
where
ref.fasta : reference in base space
ref.csfasta : reference in color space (for temporary purposes)
ref.m.fasta : reference in mock base space
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2. Convert the reads to mock base space
cs2mbs -d -r in.csfasta > in.m.fasta
where
in.csfasta : reads file in color space in.m.fasta : reads file in mock base space \-d : drop the first colorspace base during conversion. This will ignore the first color space base which is part of the primer. \-r : For each read, include the reverse of the mock base space sequence. |
3. Create SOAP indexes for the reference genome
2bwt-builder ref.m.fasta
where
ref.m.fasta : reference in mock base space |
4. Align using SOAP
soap -D ref.m.fasta.index -v 3 -a in.m.fasta -o out
where
ref.m.fasta.index : base name for the SOAP reference indexes in.m.fasta : reads file (in mock base space) out : mapping output file \-v 3 : mismatches allowed in the entire alignment |