We present Nubeam-dedup, a fast and RAM-efficient tool to de-duplicate sequencing reads
without reference genome. Nubeam-dedup represents nucleotides by matrices, transforms …

Current next generation sequencing technologies often generate duplicated or near-
duplicated reads that (depending on the application scenario) do not provide any interesting …

Removing duplicate and near-duplicate reads, generated by high-throughput sequencing
technologies, is able to reduce computational resources in downstream applications. Here …

MarkDuplicate is typically one of the most time-consuming operations in the whole genome
sequencing pipeline. Picard tool, which is widely used by biologists to sort reads in genome …

Short Structured Abstract Summary Every sequencing library contains duplicate reads.
While many duplicates arise during polymerase chain reaction (PCR), some duplicates …

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data,
and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble …

Our goal was to explore the accuracy and utility of identifying and removing PCR duplicates
from HTS data using Super Deduper. Super Deduper is a pre-alignment, sequence read …

Background During library construction polymerase chain reaction is used to enrich the DNA
before sequencing. Typically, this process generates duplicate read sequences. Removal of …

Motivation: Ultra-high-throughput sequencing produces duplicate and near-duplicate reads,
which can consume computational resources in downstream applications. A tool that …

Background Removing duplicates might be considered as a well-resolved problem in next-
generation sequencing (NGS) data processing domain. However, as NGS technology gains …