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GBCS
Je
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2594d3fc
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2594d3fc
authored
Aug 03, 2017
by
Jelle Scholtalbers
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update README and use markdown
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# 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
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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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