In the SOAP website (http://soap.genomics.org.cn/soapaligner.html#evalu2) there is the following path to run data:

Format reference sequence: <ExecutablePath>/2bwt-builder <FastaPath YourFasta="">

./2bwt-builder ~/human_genome.fa

Then under the directory there will be 13 index files, all their prefixes are yourfasta file name with “.index” added, e.g. humangenome.fa.index. The suffixes include *.amb, *.ann, *.bwt, *.fmv, *.hot, *.lkt, *.pac, *.rev.bwt, *.rev.fmv, *.rev.lkt, *.rev.pac, *.sa, and *.sai.

Alignment quick start

For alignment of single-end reads:

./soap –a <reads_a> -D index.files> -o output/output>

I got the 13 index files as described above (1), but I am not being able to set up the second command. Do I put all the 13 index files in <index.files> or that is actually the path for those files?, Do I randomly create my output files? I have 10 files for each sample, can I put them one after another in <reads_a> ? so that it runs all of them at once?.

Sorry if these are simple questions.