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BICF Cellranger mkfastq Analysis Workflow

Gervaise H. Henry; Jeremy A. Mathews; Jonathan R. Gesell; Venkat S. Malladi

BICF Cellranger mkfastq Analysis Workflow is a wrapper for the CellRanger mkfastq tool from 10x Genomics (which uses Illumina's bcl2fastq). It was developed by BICF and Strand Lab and used by the BICF at UT Southwestern Dept. of Bioinformatics.

The pipeline uses Nextflow a bioinformatics workflow tool. It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs. FastQC is run on the resulting fastq and those reports and bcl2fastq reports are collated with the MultiQC tool.

It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that Nextflow supports.

Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.

Pipeline is maintained at Git repository.

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