General outline of scripts to run

1. epiGBS/demultiplexV2.0.py

Parameters sample: --r1_in /path/to/fastq_files/R1.fq.gz --r2_in /path/to/fastq_files/R2.fq.gz --mode pe -b /path/to/barcode_files/barcodes.tsv --output-dir /path/to/outputdir --addRG -d

2. epiGBS/de_novo_reference_creation/make_reference.py

Generate de novo reference Parameters sample: --forward path/to/demultiplexed_data/R1_name_flowcell_s_lane_fastq.txt.gz --reverse path/to/demultiplexed_data/R2_name_flowcell_s_lane_fastq.txt.gz --threads 3 --outputdir /path/to/denovo/reference/denovo/ -t /tmp/ --log /path/to/denovo/reference/denovo/log_denovo.txt --samout /path/to/denovo/reference/denovo/output.sam --consensus /path/to/denovo/reference/denovo/consensus.fa --consensus_cluster /path/to/denovo/reference/denovo/consensus.clustered.fa

3. epiGBS/mapping_varcall/mapping_variant_calling.py

Generate de novo reference --tmpdir /tmp/ --input_dir /path/to/denovo/reference/denovo/ --barcodes /path/to/barcode_files/barcodes.tsv --threads 3 --output_dir /path/to/output_mapping/