J

Je

a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter read duplicates using these UMIs

Je

Additional documentation and support can be found at http://gbcs.embl.de/je

The Je tool suite

Contains

Je currently offers 4 tools :

je clip

to remove UMIs contained in reads of fastq files that do not need sample demultiplexing

je demultiplex

to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not)

je demultiplex-illu

to demultiplex fastq files according to associated index files (contain the sample encoding barcodes). Reads can additionally contain UMIs (inline)

je markdupes

to filter BAM files for read duplicates taking UMIs into account

Distributions

dist/
contains the different Je versions for download

Source

src/shell/je
is the wrapper script to call java -jar je_1.0_bundle.jar
src/galaxy/
contains the Je wrappers for Galaxy
src/test/
holds the different test data