Index of /examples/bioinformatics/oases/pipeline

Name	Last modified	Size

Parent Directory		-
outMerged/	2019-09-09 19:03	-
out_21/	2019-09-09 19:03	-
out_23/	2019-09-09 19:03	-
oases_pipeline.qsub	2019-09-09 19:03	392
test_reads.fa	2019-09-09 19:03	327K

Oases Example: run as pipeline

Oases 0.2.09 provides a script, oases_pipeline.py to simplify the steps needed to run to get the assembly. See below for its usage:


scc4% module load velvet/1.2.10

scc4% module load oases/0.2.09

print Oases pipeline command options:


scc4% oases_pipeline.py

To run oases_pipeline to get the equivalent shown in 'step_by_step' example:

kmer=21,23,2 data=test_reads.fa, read length=75bp, output directory 'out'

the output is in out_21/, out_23, and outMerged/




scc4% 
 oases_pipeline.py -m 21 -M 23 -o out -d '-short -fasta test_reads.fa'





To submit a job, execute command:



scc4% qsub -P my_project oases_pipeline.qsub





Further Resources:
For more information on how to use the software, please view Oases manual:


https://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf




Contact Information:
Research Computing Services: help@scc.bu.edu





Note: Research Computing Services (RCS) example programs are provided
"as is" without any warranty of any kind. The user assumes the entire risk of
quality, performance, and repair of any defects.  You are encouraged to copy
and modify any of the given examples for your own use.