Index of /examples/bioinformatics/oases

Name	Last modified	Size

Parent Directory		-
data/	2019-09-09 19:03	-
pipeline/	2020-05-12 10:54	-
step_by_step/	2019-09-09 19:03	-

Oases

Introduction and Notes

Oases is a de novo transcriptome assembler based on the Velvet genome assembler core. It has the similiar requirements for compiling flags as Velvet does. Like Velvet, Oases must be built with the exactly same flags used by its underlying Velvet core:

Oases on SCC was built with different compiling flags:

MAXKMERLENGTH
CATEGORIES
BIGASSEMBLY
LONGSEQUENCES
OPENMP

default version was built with the following default settings:

MAXKMERLENGTH=31
CATEGORIES=2
BIGASSEMBLY not defined
LONGSEQUENCES not defined
OPENMP not defined

currently we have another build of the following combination of flags:

MAXKMERLENGTH=149
CATEGORIES=2
BIGASSEMBLY defined
LONGSEQUENCES defined
OPENMP defined

Please use the proper build of the software according to the nature of your sequence data. If you need other different configuration flags, please contact us at help@scc.bu.edu

There are two examples for oases in this folder:

step_by_step run oases step by step based on velvet

pipeline run using oases_pipeline.py

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.