v2.0.0

CutandTag_Alignment_QC is a Snakemake workflow adapted from the protocol by Ye Zheng, Kami Ahmad, and Steven Henikoff (https://dx.doi.org/10.17504/protocols.io.bjk2kkye). This pipeline is designed to process CUT&Tag sequencing data from raw paired end FASTQ files through raw FASTQ quality control, optional adapter trimming, read alignment, optional duplicate capping, optional random downsampling, BigWig signal track generation, per sample peak calling, fragment length analysis, and QC visualization.