Article
Genetics & Heredity
Lisa Fiedler, Martin Middendorf, Matthias Bernt
Summary: A novel approach utilizing a richly annotated de Bruijn graph representation of a reference database allows for high conformity gene predictions for mitochondrial genomes. This method demonstrates better scalability than existing annotation tools and provides a fully automated means for database updates. Moreover, it can be run in parallel on multiple processors to take advantage of modern systems.
FRONTIERS IN GENETICS
(2023)
Article
Biochemical Research Methods
Mikko Rautiainen, Tobias Marschall
Summary: With the emergence of HiFi reads, De Bruijn graphs can now be efficiently constructed with a combination of long read length and low error rate. The MBG tool outperforms existing tools in building sparse De Bruijn graphs, and can quickly construct whole human genome and E.coli genome with high accuracy.
Article
Biotechnology & Applied Microbiology
Alex Di Genova, Elena Buena-Atienza, Stephan Ossowski, Marie-France Sagot
Summary: WENGAN is a genome assembler tool that produces high-quality human genome sequences at low computational cost. It achieves de novo assembly of four human genomes by combining sequencing data from multiple technologies, improving assembly contiguity and consensus quality.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F. Stadler
Summary: This study presents a novel method for detecting gene breakpoints in the nucleotide sequences of complete mitochondrial genomes, considering high substitution rates. The method uses a parallel program design and has been extensively tested for accuracy.
BMC BIOINFORMATICS
(2023)
Article
Cell Biology
Gaoyang Li, Yongzhuang Liu, Deying Li, Bo Liu, Junyi Li, Yang Hu, Yadong Wang
Summary: The deSAMBA approach proposed in this study fills the gap in fast and accurate classification tools for noisy long reads, which is a bottleneck in utilizing long-read metagenomic sequencing technologies. It outperforms state-of-the-art tools by achieving high yields and fast speed simultaneously, demonstrating great potential for cutting-edge metagenomics studies.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Microbiology
Julie Callanan, Stephen R. Stockdale, Andrey Shkoporov, Lorraine A. Draper, R. Paul Ross, Colin Hill
Summary: The human gut is colonized by a diverse range of microbes, including viruses, which have recently attracted more attention in research. Different viral extraction protocols used in studies can introduce biases affecting overall conclusions, highlighting the need for clearly outlining protocol variations and perhaps establishing an unbiased and standardized method for examining the viral component of the human microbiome.
Article
Biotechnology & Applied Microbiology
Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro
Summary: The de Bruijn graph plays a crucial role in computational genomics, and Cuttlefish 2 significantly improves its construction efficiency. It can quickly construct large-scale genomic graphs with reduced time and memory usage, outperforming current competitors.
Article
Biochemistry & Molecular Biology
Markella Moraitou, Adrian Forsythe, James A. Fellows Yates, Jaelle C. Brealey, Christina Warinner, Katerina Guschanski
Summary: In this study, the oral microbiomes of three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) were investigated using shotgun metagenomics of 46 museum-preserved dental calculus samples. The researchers found that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Altitudinal differences in gorilla subspecies ranges appeared to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. The presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa further supported this. The study also found a high abundance of nitrate-reducing oral taxa in mountain gorillas, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Mingzhu Sun, Erli Pang, Wei-Ning Bai, Da-Yong Zhang, Kui Lin
Summary: Polyploidy is common and its effects are complex and variable. Computational tools for ploidy estimation are urgently needed to avoid cumbersome experiments. We developed ploidyfrost, a method for estimating ploidy levels without a reference genome, and evaluated its performance using different samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Jarno Alanko, Bahar Alipanahi, Jonathen Settle, Christina Boucher, Travis Gagie
Summary: The de Bruijn graph is a widely used graph model for biological data, with several methods for building and representing it. However, compressed and compact de Bruijn graphs have limitations in updating. The recent BufBOSS method addresses this issue by buffering data, achieving attractive trade-offs in terms of time, memory, and disk, with superior deletion performance.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Nozomi Hasegawa, Kana Shimizu
Summary: This study proposes an accurate coloring method that reduces the generation of read-incoherent paths by using different colors for a single read based on its position. Experimental results show that our method significantly reduces the occurrence of read-incoherent paths and achieves comparable construction time, peak memory size, and index size to the previous method.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Cell Biology
Yanfei Li, Yueling Jin, Jianming Zhang, Haoying Pan, Lan Wu, Dingsheng Liu, Jinlong Liu, Jing Hu, Junwei Shen
Summary: The study established an effective extraction method to obtain high quality gut microbiota genomes, identifying several new bacterial species including a new conditional pathogen, Enterococcus tongjius. The research provides a novel and reliable approach to recover gut microbiota genomes, aiding in the discovery of new bacteria species and advancing understanding of the microbiome underlying human health and diseases.
CELL DEATH & DISEASE
(2021)
Article
Computer Science, Artificial Intelligence
Firaol Dida, Gangman Yi
Summary: This article explores the rapid growth of high-throughput sequencing projects and new read-assembly algorithms driven by next-generation sequencing technologies like Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for various organisms, with de novo assembly playing a crucial role in gene discovery and other studies. The article provides a thorough comparison of different assembly algorithms to aid new users in understanding them better.
PEERJ COMPUTER SCIENCE
(2021)
Article
Computer Science, Artificial Intelligence
Zeinab Zare Hosseini, Shekoufeh Kolahdouz Rahimi, Esmaeil Forouzan, Ahmad Baraani
Summary: Genome assembly is the computational process of merging short parts of DNA into larger sequences. The shift to distributed memory systems has become necessary due to the rapid growth of high-throughput genome sequencing technologies. The DRMI-DBG model proposed in this paper is a scalable iterative de Bruijn Graph framework that utilizes the power of Spark and Giraph to parallelize the construction and processing of de Bruijn graphs on distributed memory systems. Experimental results show that DRMI-DBG accelerates the performance of existing algorithms while maintaining or improving the quality of the assembly.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Microbiology
Jiaqi Zeng, Yuxiao Wang, Ziyao Wu, Yizhuang Zhou
Summary: FRAGTE2 is an efficient genome sieving algorithm that significantly reduces computing costs and improves sensitivity and specificity. It is suitable for prokaryotic species demarcation.
FRONTIERS IN MICROBIOLOGY
(2022)