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Genome assembly in the telomere-to-telomere era
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly — the process of reconstructing the genome...
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De novo genome assembly of the invasive mosquito species Aedes japonicus and Aedes koreicus
BackgroundRecently, two invasive Aedes mosquito species, Ae. japonicus and Ae. koreicus , are circulating in several European countries posing...
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SnakeCube: containerized and automated pipeline for de novo genome assembly in HPC environments
ObjectiveThe rapid progress in sequencing technology and related bioinformatics tools aims at disentangling diversity and conservation issues through...
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A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome
Advances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have...
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Software evaluation for de novo detection of transposons
Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite...
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Leucoma salicis nucleopolyhedrovirus (LesaNPV) genome sequence shed new light on the origin of the Alphabaculovirus orpseudotsugatae species
LesaNPV (Leucoma salicis nucleopolyhedrovirus) is an alphabaculovirus group Ib. Potentially, it can be an eco-friendly agent to control the white...
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Variant calling and benchmarking in an era of complete human genome sequences
Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing...
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Next-Generation Sequencing
The next-generation sequencing platforms can generate a large amount of high-throughput sequencing data in a short span of time. Reference-based...
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Current Progress of Bioinformatics for Human Health
Massive biological data provides a broad view to understand the dynamics of human health status and disease from multiple aspects. During the past...
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The Dfam community resource of transposable element families, sequence models, and genome annotations
Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (
https://dfam.org ...
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Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics
Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de...
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Using Apache Spark on genome assembly for scalable overlap-graph reduction
BackgroundDe novo genome assembly is a technique that builds the genome of a specimen using overlaps of genomic fragments without additional work...
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SRTdb: an omnibus for human tissue and cancer-specific RNA transcripts
The production of functional mature RNA transcripts from genes undergoes various pre-transcriptional regulation and post-transcriptional...
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Genomic analyses implicate noncoding de novo variants in congenital heart disease
A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo...
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Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395
BackgroundKlebsiella pneumoniae , which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant...
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The First Genome-Wide Survey of Shortbelly Eel (Dysomma anguillare Barnard, 1923) to Provide Genomic Characteristics, Microsatellite Markers and Complete Mitogenome Information
Dysomma anguillare is a demersal eel widespread distributing in tropical waters of the Indo-West Pacific and Atlantic. As an important component of...
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ViralVectors: compact and scalable alignment-free virome feature generation
AbstractThe amount of sequencing data for SARS-CoV-2 is several orders of magnitude larger than any virus. This will continue to grow geometrically...
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Bioinformatics Algorithms and Software for Predicting Microbiomes
Over the last decade, bioinformatics approaches have been used extensively for analyzing microbiomes from various sources. Microbiomes can vary from...
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A comprehensive investigation of metagenome assembly by linked-read sequencing
BackgroundThe human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial...
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Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases
BackgroundHaploinsufficiency of the transcription factor PAX6 is the main cause of congenital aniridia, a genetic disorder characterized by iris and...
