Abstract The Next-Generation Sequencing (NGS) platforms produce massive amounts of
data to analyze various features in environmental samples. These data contain multiple …

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

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 …

Abstract The Next-Generation Sequencing (NGS) platforms provide a major approach to
obtaining millions of short reads from samples. NGS has been used in a wide range of …

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

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

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

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 Read-merging algorithms that look solely at the reads can misalign and mis-
merge the reads (especially near repetitive sequences). Results The C++ program …

Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient
alternative to traditional Sanger sequencing and is widely used in both de novo whole …