This is a Split-seq Scell Data analysis method. This pipeline can process the over 20000 cells in 3 days. http://science.sciencemag.org/content/360/6385/176.full
##Useage pipeline:
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first step:
files perpare: raw fastq files and barcode file change your paire-end fastq files name to R1.fastq(R1) and R2.fastq(R2) -
then run:
init.sh to initialize the directy and environment.