README¶
install¶
sprai requres
- zlib
- blast+ ver. 2.2.27 or newer
- Celera Assembler (if you assemble)
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 &