INCLIVA - MAESTER

This pipeline is partially based on the methodology described in the paper by Miller et al. (2022), Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations (Nat Biotechnol 40, 1030–1034). The original code and methods have been optimized to improve performance and efficiency. For more details, see: https://doi.org/10.1038/s41587-022-01210-8

Repository strucuture is as following:

maester_pipeline/
├── analyze_variant
│   └── explore_variants_final.r
├── get_HQ_barcodes.R
├── parse_metrics_slurm.py 
├── processing_pipeline
│   ├── inc_assemble_fastq.R
│   ├── inc_calculate_coverage_cut.R
│   ├── inc_create_af_dp_table.R
│   ├── inc_parse_vcf_lofreq.py
│   ├── inc_split_bam.py
│   ├── MAESTER_slurm.conf
│   └── MAESTER_slurm.sh
└── README.md

• analyze_variant/

  • explore_variants_final.r: Used to explore and extract informative variants obtained through MAESTER_slurm.sh. Also generates several plots.

• get_HQ_barcodes.R: Obtains HQcb (High Quality cell-barcodes) from a scRNA-seq object.

• parse_metrics_slurm.py: Calculates several quality statistics from a MAESTER_slurm.sh execution.

• processing_pipeline/

  • inc_assemble_fastq.R: Assembles FASTQ files for high-quality cells from raw data (used in MAESTER_slurm.sh).
  • inc_calculate_coverage_cut.R: Calculates the "good quality coverage" threshold in HQcb (used in MAESTER_slurm.sh).
  • inc_create_af_dp_table.R: Creates an allele frequency and depth table for all variants in all cells (used in MAESTER_slurm.sh).
  • inc_parse_vcf_lofreq.py: Corrects lofreq VCF format (used in MAESTER_slurm.sh).
  • inc_split_bam.py: Splits the MAESTER BAM file into one BAM per HQcb (used in MAESTER_slurm.sh).
  • MAESTER_slurm.conf: Configuration file with paths, software, and parameters (used with MAESTER_slurm.sh).
  • MAESTER_slurm.sh: Main script for processing and analyzing MAESTER data.

• README.md