This tool is an automated pipeline for preprocessing single-cell genomics data. It is designed to take raw data (fastq files) from a variety of single-cell genomics platforms and a seqspec file as input, and output a count matrix (RNA) or a fragment file (ATAC) for downstream analysis. The seqspec files for common platforms can be found here: https://github.com/IGVF/seqspec.
pip install precellar
pip install 'git+https://github.com/regulatory-genomics/precellar.git#egg=precellar&subdirectory=python'
For more information, please refer to the documentation: https://lab.kaizhang.org/precellar/.