PiledUp

Piledup is a term that appears in multiple domains, most prominently in bioinformatics. In genomics, piledup (often written as pileup) refers to a situation in which many sequencing reads align to the same genomic coordinate, producing a pile of evidence at that position. This pileup is used to summarize data for downstream analyses such as variant calling, genotype likelihood estimation, or depth-of-coverage assessment. The concept is typically represented as a per-base pileup, listing the bases observed at a position and their counts.

In sequencing workflows, pileups are generated from aligned reads and are commonly visualized or stored in formats such as mpileup or per-base summaries extracted from BAM files. Accurate interpretation depends on data quality and accounting for biases, including sequencing errors, alignment artifacts, and PCR duplicates. Deduplication methods, including marking duplicates or using unique molecular identifiers (UMIs), are applied to reduce redundant evidence and improve downstream inferences.

Outside genomics, piledup may be used informally to describe the aggregation or deduplication of identical items in data processing pipelines. The term is not standardized and its meaning can vary by context, so clarification is often required when encountered in literature or software documentation.

See also: Pileup, mpileup, sequencing depth, SAM/BAM format, duplicate read, UMI.