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

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

The presence of duplicates introduced by PCR amplification is a major issue in paired short
reads from next-generation sequencing platforms. These duplicates might have a serious …

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 …

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 …

Abstract Background Advances in Illumina DNA sequencing technology have produced
longer paired-end reads that increasingly have sequence overlaps. These reads can be …

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 …

Motivation: Identifying subclonal mutations and their implications requires accurate
estimation of mutant allele fractions from possibly duplicated sequencing reads. Removing …