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Short-Read RNA-Seq
RNA sequencing (RNA-Seq) has emerged as a powerful and versatile tool for the comprehensive analysis of transcriptomes and has been widely used to...
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Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes...
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ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
BackgroundStructural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external...
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Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data
Viral metagenomics enables the detection, characterization, and quantification of viral sequences present in shotgun-sequenced datasets of purified...
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Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches
BackgroundThe application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and...
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Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model
BackgroundVariable number tandem repeats (VNTRs) are highly polymorphic DNA regions harboring many potentially disease-causing variants. However,...
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Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates
BackgroundOxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However,...
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Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene
GBA variants carriers are at increased risk of Parkinson’s disease (PD) and Lewy body dementia (LBD). The presence of pseudogene GBAP1 predisposes to...
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Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
BackgroundReproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and...
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METASEED: a novel approach to full-length 16S rRNA gene reconstruction from short read data
BackgroundWith the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error...
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ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs
BackgroundTranscriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies...
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De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the...
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High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly
BackgroundDespite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the...
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Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation
Key messageStructural variants (SV) of 23 barley inbreds, detected by the best combination of SV callers based on short-read sequencing, were...
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RResolver: efficient short-read repeat resolution within ABySS
BackgroundDe novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for...
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Insights into the genome of the ‘Loco’ Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae
BackgroundThe Peruvian ‘chanque’ or Chilean ‘loco’ Concholepas concholepas is an economically, ecologically, and culturally important muricid...
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Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
BackgroundDirect RNA sequencing (dRNA-seq) on the Oxford Nanopore Technologies (ONT) platforms can produce reads covering up to full-length gene...
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Impact of short-read sequencing on the misassembly of a plant genome
BackgroundAvailability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome...
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Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine
PacBio long-read sequencing is a third-generation technology that generates long reads up to 20 kilobases (kb), unlike short-read sequencing...