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Genome sequence assembly algorithms and misassembly identification methods
The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. Assembly...
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Mechanism of autocatalytic activation during proteasome assembly
Many large molecular machines are too elaborate to assemble spontaneously and are built through ordered pathways orchestrated by dedicated...
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Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Despite advances in long-read sequencing technologies, constructing a near telomere-to-telomere assembly is still computationally demanding. Here we...
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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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High-quality metagenome assembly from long accurate reads with metaMDBG
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an...
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Assembly Theory: What It Does and What It Does Not Do
A recent publication in Nature has generated much heated discussion about evolution, its tendency towards increasing diversity and complexity, and...
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Sequencing and Assembly of Polyploid Genomes
Polyploidy has been observed throughout major eukaryotic clades and has played a vital role in the evolution of angiosperms. Recent polyploidizations...
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Haplotype-resolved assembly of diploid genomes without parental data
Routine haplotype-resolved genome assembly from single samples remains an unresolved problem. Here we describe an algorithm that combines PacBio HiFi...
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NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads
Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we...
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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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Mabs, a suite of tools for gene-informed genome assembly
BackgroundDespite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds...
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Biotemplated precise assembly approach toward ultra-scaled high-performance electronics
Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and...
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Telomere-to-telomere assembly of diploid chromosomes with Verkko
The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this...
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Algorithm for DNA sequence assembly by quantum annealing
BackgroundThe assembly task is an indispensable step in sequencing genomes of new organisms and studying structural genomic changes. In recent years,...
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Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly
BackgroundDiverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production...
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Structure and assembly of the NOT10:11 module of the CCR4-NOT complex
NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this...
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Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling
BackgroundPan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic...
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Polymeric nature of tandemly repeated genes enhances assembly of constitutive heterochromatin in fission yeast
Motivated by our recent experiments that demonstrate that the tandemly repeated genes become heterochromatin, here we show a theory of...
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Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics
BackgroundSweet yellow clover ( Melilotus officinalis ) is a diploid plant (2n = 16) that is native to Europe. It is an excellent legume forage. It...
