| If you have barcodes and/or UMIs in your fastq files, you'll most likely enjoy Je. Je currently offers 4 tools: demultiplex to demultiplex multi-samples fastq files which reads contain barcodes and UMIs (or not) demultiplex-illu to demultiplex fastq files according to associated index files (contain the sample encoding barcodes). Reads can additionally contain UMIs (inline) clip to remove UMIs contained in reads of fastq files that do not need sample demultiplexing markdupes to filter BAM files for read duplicates taking UMIs into account |
hg clone https://toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/suite_je