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GTax: improving de novo transcriptome assembly by removing foreign RNA contamination
The cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a...
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transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
BackgroundRNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but...
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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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De novo genome assembly of a high-protein soybean variety HJ117
ObjectivesSoybean is an important feed and oil crop in the world due to its high protein and oil content. China has a collection of more than 43,000...
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De novo transcriptome assembly of the oak processionary moth Thaumetopoea processionea
ObjectivesThe oak processionary moth (OPM) ( Thaumetopoea processionea ) is a species of moth (order: Lepidoptera ) native to parts of central Europe....
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A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus
Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global...
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High-quality chromosome-level de novo assembly of the Trifolium repens
BackgroundWhite clover ( Trifolium repens L. ), an excellent perennial legume forage, is an allotetraploid native to southeastern Europe and southern...
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Transcriptome Data Analysis Using a De Novo Assembly Approach
Characterization and profiling of the gene expression data or, more formally, called transcriptome are crucial steps in revealing the involvement of...
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Long-read Sequencing and de novo Genome Assembly of Three Aspergillus fumigatus Genomes
Aspergillus fumigatus is a genetically diverse fungal species, which is near ubiquitous in its global distribution and is the major cause of the...
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An External Memory Approach for Large Genome De Novo Assembly
De novo genome assembly of sequenced reads is a fundamental problem in bioinformatics. When there is no reference genome sequence to guide the...
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Accurate long-read de novo assembly evaluation with Inspector
Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly...
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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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Transcriptome sequencing of the endangered land snail Karaftohelix adamsi from the Island Ulleung: De novo assembly, annotation, valuation of fitness genes and SSR markers
BackgroundThe Bradybaenidae snail Karaftohelix adamsi is endemic to Korea, with the species tracked from Island Ulleung in North Gyeongsang Province...
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Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability
Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication...
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A combined de novo assembly approach increases the quality of prokaryotic draft genomes
Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes...
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phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
Haplotype-aware diploid genome assembly is crucial in genomics, precision medicine, and many other disciplines. Long-read sequencing technologies...
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De novo genome assembly and annotation of the medicinal plant Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thom’s
Indian natural climbing shrub Tinospora cordifolia , often known as “Guduchi” and “Amrita,” is a highly esteemed medicinal plant in the Indian system...
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De novo transcriptome assembly reveals characteristics of flower sex determination of Excoecaria agallocha
Key messageMADS-box genes family may play important roles in the flower sex determination in Excoecaria agallocha . A total of 73 MADS-box genes were...
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De novo assembly and annotation of the singing mouse genome
BackgroundDevelo** genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex...
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A de novo long-read genome assembly of the sacred datura plant (Datura wrightii) reveals a role of tandem gene duplications in the evolution of herbivore-defense response
The sacred datura plant (Solanales: Solanaceae: Datura wrightii ) has been used to study plant–herbivore interactions for decades. The wealth of...
