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