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.
- To get started using SOAP, visit the SOAP website.
How to run SOAP
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
2. Convert the reads to mock base space
cs2mbs -d -r in.csfasta > in.m.fasta
3. Create SOAP indexes for the reference genome
4. Align using SOAP
soap -D ref.m.fasta.index -v 3 -a in.m.fasta -o out
- If you have lots of warning message as 'length y < 0, countinue as 13', it means that your read length is too short, so SOAP cannot handle them properly. Currently, SOAP supports only reads longer than 30 bp.( NewsGroup article; it described 2.18 version, but 2.20 shows the same result.)