README

install

sprai requres

When you install Celera Assembler, you need to change one line. In AS_global.h in the src directory of Celera Assembler, change from

#define AS_READ_MAX_NORMAL_LEN_BITS 11

to

#define AS_READ_MAX_NORMAL_LEN_BITS 15

For details, please read pacbiotoca wiki

After the requirements are satisfied,

cd sprai
./waf configure [--prefix=/some/dir/]
./waf build
./waf install

If you specify –prefix=/some/dir/, sprai will be installed in /some/dir/bin/ directory. If you don’t, it will be installed in /usr/local/bin.

uninstall

cd sprai
./waf uninstall

run sprai

mkdir tmp
cd tmp
ln -s target_CLRs.fastq all.fq
cp /path/to/sprai/asm.spec .
cp /path/to/sprai/ec.spec .

one node mode

Open ec.spec by an editor and specify a ca_path parameter the directory in which you put wgs-assembler binaries.

You must change estimated_genome_size. If you cannot estimate the length of your target genome, give a large number (ex. 1e+12).

Modify other parameters in ec.spec for your needs following instructions in the file. Then,

fs2ctg_v4.pl ec.spec asm.spec > fs2ctg_v4.log 2>&1 &

This will do error correction and make contigs.

If you use error corrected reads and does not assemble, do

fs2ctg_v4.pl ec.spec asm.spec -ec_only > fs2ctg_v4.log 2>&1 &

many node mode

If you would like to use SGE to correct errors of CLRs and assemble, specify blast_path and sprai_path in ec.spec, and do

ezez4qsub_v6.pl ec.spec asm.spec > ezez4qsub_v6.log 2>&1 &

If you use error corrected reads and does not assemble, do

ezez4qsub_v6.pl ec.spec asm.spec -ec_only > ezez4qsub_v6.log 2>&1 &

many node mode 2

If you use TGEW,

ezez4makefile.pl ec.spec asm.spec > ezez4makefile.log 2>&1
tge_make > tge_make.log 2>&1 &

or

ezez4makefile.pl ec.spec asm.spec > ezez4makefile.log 2>&1
tge_make > tge_make.log 2>&1 &