![]() ![]() ![]() A typical CIPHER workflow includes: (1) raw sequence evaluation, (2) read trimming and adapter removal, (3) read mapping and quality filtering, (4) visualization track generation, and (5) extensive quality control assessment. CIPHER’s pipelines conduct extensive quality and contamination control checks, as well as comprehensive downstream analysis. CIPHER implements various open source software packages, in-house scripts, and Docker containers to analyze and process single-ended and pair-ended datasets. We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. ![]() Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. ![]()
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