NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows.¶
- A bioinformatics workflow (WF) is a series of computer programs called sequentially, sometimes on hundreds or even thousands of samples.
- NeatSeq-Flow creates human readable and self explanatory shell scripts for execution on computer grids.
- The hyrachically-organised scripts are then executed by running a master-script.
- The main benefits in using NeatSeq-Flow are:
- the user has full control over the WF execution;
- the cluster job scheduler ensures correct execution order and enforces dependencies;
- simple, cross-platform installation;
- scripts and output files are neatly organized;
- utilization of cluster parallelization capabilities;
- documentation, version control as well as time & memory usage reports and
- adding modules and expanding existing WFs requires only basic python skills.
- NeatSeq-Flow is available on github (See Download and Install)
- A GUI is available for parameter and sample file editting and NeatSeq-Flow execution.
While a basic number of modules come with NeatSeq-Flow, the main source of modules is the NeatSeq-Flow module and workflow repository. This repository is available on github. Check out the list of modules in the modules repository.
- The National Knowledge Center for Rare / Orphan Diseases.
- Faculty of Agriculture, Food and Environment