ashvark / Je

a suite to handle barcoded fastq files with (or without) Unique Molecule Identifiers (UMIs) and filter read duplicates using these UMIs

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 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