Related papers: genomepy: genes and genomes at your fingertips
The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…
Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, high throughput sequencing.…
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…
The Genome Warehouse (GWH), accessible at https://ngdc.cncb.ac.cn/gwh, is an extensively utilized public repository dedicated to the deposition, management and sharing of genome assembly sequences, annotations, and metadata. This paper…
Genomic data has become increasingly accessible to the general public with the advent of companies offering whole genome sequencing at a relatively low cost. However, their reports are not verifiable due to a lack of crucial details and…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
While the publication of datasets in scientific repositories has become broadly recognised, the repositories tend to have increasing semantic-related problems. For instance, they present various data reuse obstacles for machine-actionable…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Cheap high-throughput DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food…
Summary: Data management in clinical metabolomics studies is often inadequate. To improve this situation we created LabPipe to provide a guided, customisable approach to study-specific sample collection. It is driven through a local client…
Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for…
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
Summary: HTSeq 2.0 provides a more extensive API including a new representation for sparse genomic data, enhancements in htseq-count to suit single cell omics, a new script for data using cell and molecular barcodes, improved documentation,…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
The availability of genomic data is essential to progress in biomedical research, personalized medicine, etc. However, its extreme sensitivity makes it problematic, if not outright impossible, to publish or share it. As a result, several…
We linked names and contact information to publicly available profiles in the Personal Genome Project. These profiles contain medical and genomic information, including details about medications, procedures and diseases, and demographic…
Metagenomics offers a way to analyze biotopes at the genomic level and to reach functional and taxonomical conclusions. The bio-analyzes of large metagenomic projects face critical limitations: complex metagenomes cannot be assembled and…