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Molluscan Genomics: Implications for Biology and Aquaculture
Purpose of ReviewAs a result of advances in DNA sequencing technology, molluscan genome research, which initially lagged behind that of many other...
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Konnector v2.0: pseudo-long reads from paired-end sequencing data
BackgroundReading the nucleotides from two ends of a DNA fragment is called paired-end tag (PET) sequencing. When the fragment length is longer than...
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A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses
BackgroundNext-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral...
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Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction
The emergence of apomixis—the transition from sexual to asexual reproduction—is a prominent feature of modern citrus. Here we de novo sequenced and...
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Optimized Illumina PCR-free library preparation for bacterial whole genome sequencing and analysis of factors influencing de novo assembly
BackgroundNext-generation sequencing (NGS) technology has paved the way for rapid and cost-efficient de novo sequencing of bacterial genomes. In...
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Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus
BackgroundAphids are major vectors of plant viruses. Common bean ( Phaseolus vulgaris L.) and maize ( Zea mays L.) are important crops that are...
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Xander: employing a novel method for efficient gene-targeted metagenomic assembly
BackgroundMetagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be...
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Genomic and transcriptomic heterogeneity in metaplastic carcinomas of the breast
Metaplastic breast cancer (MBC) is a rare special histologic type of triple-negative breast cancer, characterized by the presence of neoplastic cells...
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Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers
Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and...
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Genetic variation and the de novo assembly of human genomes
The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology....
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Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads
BackgroundMicrobiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the...
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New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali
BackgroundEncoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate...
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Improved genome inference in the MHC using a population reference graph
Although much is known about human genetic variation, such information is typically ignored in assembling new genomes. Instead, reads are mapped to a...
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De novo construction of a “Gene-space” for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources
BackgroundThe continuing increase in size and quality of the “short reads” raw data is a significant help for the quality of the assembly obtained...
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Shotgun Metagenomic Sequencing Analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities
Shotgun metagenomic sequencing of bacterial communities in necrotic plant lesions allows insights of host–pathogen molecular interactions. Soft-rot...
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The Impact of Drought Stress on the Quality of Spice and Medicinal Plants
This review addresses the well known phenomenon that spice and medicinal plants grown under semi-arid conditions generally reveal significantly...
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The Molecular Blueprint of a Fungus by Next-Generation Sequencing (NGS)
Sequencing the whole genome of an organism is invaluable for its comprehensive molecular characterization and has been drastically facilitated by the...
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SNP Discovery Using Next Generation Transcriptomic Sequencing
In this chapter, I will guide the user through methods to find new SNP markers from expressed sequence (RNA-Seq) data, focusing on the sample...
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Whole-Genome Sequencing Recommendations
Recent technological developments have revolutionized the way we perform genetic analyses. In particular whole-genome sequencing provides access to...
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A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers
Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast...
