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# Je

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The main public repository is at [github](https://github.com/gbcs-embl/Je/) where issues or pull request can be created.

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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

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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.
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* **je clip**

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

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* **je markdupes**

 	filters BAM files for read duplicates taking UMIs into account.

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* **je demultiplex**

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

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

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    is the wrapper script to call ``java -jar je_*_bundle.jar``
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* ``src/galaxy/``

    contains the Je wrappers for Galaxy

* ``src/test/``

    holds the different test data