Je

The main public repository is at github where issues or pull request can be created.

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

Installation

• Install from the bioconda channel with conda install -c bioconda je-suite
• Or, download the je_<version>.tar.gz from the dist/ directory and unpack

The Je tool suite

Je currently offers the following tools:

• je debarcode

  demultiplexes multi-samples fastq files using user-defined input read-layouts and write output files following user-defined output-layouts. Replaces both demultiplex-illu and demultiplex since version 2.0.

• je dropseq

  to process drop-seq results: clips cell barcode and UMI from read 1 and adds them to header of read 2 (a unique output fastq is created).

• je retag

  extracts barcode(s) and UMI sequence(s) embedded in read names of a BAM file and migrate them to proper BAM tags.

• je clip

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

• je markdupes

  filters BAM files for read duplicates taking UMIs into account.

• je demultiplex

  to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not). Deprecated since version 2.0 (use je debarcode instead).

• je demultiplex-illu

  to demultiplex fastq files according to associated index files (contain the sample encoding barcodes). Reads can additionally contain UMIs (inline). Deprecated since version 2.0 (use je debarcode instead).

Distributions

• dist/

  contains the different Je versions for download

• Bioconda

  starting from version 1.2 je-suite can be installed through conda: https://anaconda.org/bioconda/je-suite

Source

• src/shell/je

  is the wrapper script to call java -jar je_*_bundle.jar

• src/galaxy/

  contains the Je wrappers for Galaxy

• src/test/

  holds the different test data