Published in GigaScience
Background The main goal of this collaborative effort is to provide genome-wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented ind...
Published in GigaScience
Background Genome mining for biosynthetic gene clusters (BGCs) has become an integral part of natural product discovery. The >200,000 microbial genomes now publicly available hold information on abundant novel chemistry. One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification o...
Published in GigaScience
Background The evolving antibiotic-resistant behavior of health care–associated methicillin-resistant Staphylococcus aureus (HA-MRSA) USA100 strains are of major concern. They are resistant to a broad class of antibiotics such as macrolides, aminoglycosides, fluoroquinolones, and many more. Findings The selection of appropriate antibiotic susceptib...
Published in GigaScience
Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free assemblies is therefore the ultimate, but sadly still unachieved goal of a multitude of research projects. Despite the ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably gener...
Published in GigaScience
Background Argiope bruennichi , the European wasp spider, has been investigated intensively as a focal species for studies on sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. ...
Published in GigaScience
Background Galaxy is a web-based and open-source scientific data-processing platform. Researchers compose pipelines in Galaxy to analyse scientific data. These pipelines, also known as workflows, can be complex and difficult to create from thousands of tools, especially for researchers new to Galaxy. To help researchers with creating workflows, a s...
Published in GigaScience
Background Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female...
Published in GigaScience
Background The development of high-throughput sequencing and genotyping methodologies has enabled the identification of thousands of genomic regions associated with several complex traits. The integration of multiple sources of biological information is a crucial step required to better understand patterns regulating the development of these traits...
Published in GigaScience
Background Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free RNAs contained within the input solution are also captured by these assays. This sequencing of cell-free RNA constitutes a background contamination that confounds the biological interpretation of single-cell trans...
Published in GigaScience
Background Structural variants (SVs) are critical contributors to genetic diversity and genomic disease. To predict the phenotypic impact of SVs, there is a need for better estimates of both the occurrence and frequency of SVs, preferably from large, ethnically diverse cohorts. Thus, the current standard approach requires the use of short paired-en...
