Built-in modules of Eoulsan

Eoulsan contains several built-in modules to perform analysis. As Eoulsan can work in local and distributed modes, some modules are available for the two and some for only one. Note that local Hadoop cluster mode and AWS mode are both distributed modes.

Phase/Module Local Mode Distributed mode Comment
Create mapper index Yes Yes This module is automatically called when need
Create STAR mapper index Yes Yes
FastQC Yes Yes
Filter reads Yes Yes
Map reads Yes Yes
Filter alignments Yes Yes
Filter and map reads No Yes
Sam2bam Yes Yes
Bam2sam Yes Yes
Sam2fastq Yes Yes
Splice2bed Yes Yes
Expression Yes Yes
Expression annotation Yes Yes
MultiQC Yes Yes
Normalization Yes No
Differential analysis Yes No
Differential analysis with DESeq2 Yes No
Differential analysis annotation Yes No
R SingleCellExperiment creator Yes No
Splitters and mergers Yes No
Shell Yes No
Import Yes No