Motivation Genome sequencing experiments have revolutionized molecular biology by
allowing researchers to identify important DNA-encoded elements genome wide. Regions …

ChIP-seq is one of the core experimental resources available to understand genome-wide
epigenetic interactions and identify the functional elements associated with diseases. The …

Abstract Motivation Unique molecular identifiers (UMIs) are added to DNA fragments before
PCR amplification to discriminate between alleles arising from the same genomic locus and …

A key step in the transformation of raw sequencing reads into biological insights is the
trimming of adapter sequences and low-quality bases. Read trimming has been shown to …

Next-generation sequencing: adjusting to data overload | Nature Methods Skip to main content
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The year 2022 will be remembered as the turning point for accurate long-read sequencing,
which now establishes the gold standard for speed and accuracy at competitive costs. We …

Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is
a technique widely used to investigate genome-wide chromatin accessibility. The recently …

Structural variations (SVs) are large genomic rearrangements that vary significantly in size,
making them challenging to detect with the relatively short reads from next-generation …

Large-scale sequencing techniques to chart genomes are entirely consolidated. Stable
computational methods to perform primary tasks such as quality control, read mapping, peak …

Motivation ChIP-seq detects protein–DNA interactions within chromatin, such as that of
chromatin structural components and transcription machinery. ChIP-seq profiles are often …