Build index files for the reference genome before running SOAP
This tools is part of SOAP (Short Oligonucleotide Analysis Package).
To run SOAPaligner, we need to build index files for the reference genome, and then search reads against the formatted index files.
Then under the directory there will be 13 index files, all their prefixes are your_fasta file name with “.index” added, e.g. human_genome.fa.index. The suffixes include *.amb, *.ann, *.bwt, *.fmv, *.hot, *.lkt, *.pac, *.rev.bwt, *.rev.fmv, *.rev.lkt, *.rev.pac, *.sa, and *.sai.