Commit 2594d3fc by Jelle Scholtalbers

update README and use markdown

parent 563fb7e1
# Je
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 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
* 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_1.0_bundle.jar``
* ``src/galaxy/``
contains the Je wrappers for Galaxy
* ``src/test/``
holds the different test data
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
\ No newline at end of file
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