SOAP

soap2sam.pl

>wget http://soap.genomics.org.cn/down/soap2sam.tar.gz

soapaligner

>wget http://soap.genomics.org.cn/down/SOAPaligner-v2.20-Linux-x86_64.tar.bz2

#soap's index-builder "2bwt-builder" do not accept wildcard.

>2bwt-builder *.fa #will not work, only build the indexes for the first .fa file. As thus we need to make a single .fa file.

#create a single .fa file

>cat *.fa>> hg19.fa # ~3.2GB

#HG19 has 93 fasta entry

>grep -c '>' hg19.fa

93

#now build the index files

>2bwt-builder hg19.fa

Parsing FASTA file..

Finished. Parsed 93 sequences.

Elapsed time = 77.96 s

Building Look-Up..

Finished.

Elapsed time = 250.56 s

Building BWT..

Finished constructing BWT in 292 iterations. Elapsed time = 1354.80 s

Saving BWT..

Finished saving BWT. Elapsed time = 1.02 s

Building Reversed BWT..

Finished constructing Reversed BWT in 292 iterations. Elapsed time = 1360.44 s

Saving BWT..

Finished saving BWT. Elapsed time = 7.29 s

Loading BWT...

Finished loading BWT. Elapsed time = 3.86 s

Building SA value...

Finished building SA value. Elapsed time = 1028.20 s

Building High-Occ Hash Table...

Finished.

Elapsed time = 695.12 s

Building SA index...

Finished building SA index. Elapsed time = 14.29 s

Index building is completed.

Total elapsed time = 4793.76 s