A genome assembly is the specific set of nucleotide sequences used to represent an organism's genome. Multiple sequencing groups may produce different genome assemblies for the same organism and any one group may release different versions of an assembly as they generate more sequence data, close gaps, correct misassemblies or make other improvements to the assembly.
Allows users to compare, visualize and summarize genome and marker genes. POGO-DB contains a graphical interface on which it is possible to visualize the information. This database provides user a way in which to notice marker genes that best recapitulate genome relatedness. It also compares different aspects of genome relatedness. The database gets computational resources to generate with raw BLAST results.
Offers a draft de novo assembly of the gorilla Y Chromosome. GorillaY was create by using an integrated strategy to sequence and assemble the gorilla Y Chromosome. The Y Chromosome-specific reads was extracted by using an algorithm developed in-house, RecoverY. Approximately 12,000 copies of the Y Chromosome were flow sorted from a fibroblast cell line of western lowland gorilla male.
Provides continuous, objective and reproducible evaluation of genome assemblers using docker containers. nucleotid.es compares how different genome assemblers perform against a variety of test sequence data. Multiple different benchmarks show the average performance of each assembler. Every genome assembler is examined as a self-contained Docker application. These containers eliminate the common problem in bioinformatics where the software won't compile or requires multiple additional dependencies. Furthermore, users can pull an assembler from the docker repository and start using it immediately and developers are encouraged to send their assembler to be included in the benchmarks.
Deals with Tibetan hulless barley. QGD consists of a repository giving access to multiple genome assemblies (such as one combining third generation sequencing (TGS) and next generation sequencing (NGS) and genome annotation including protein-coding genes prediction. The database gives access to a browser with multiple filters, a set of downloadable files as well as several links related with the study of barley.
Aims to provide access to all available assembled genomes and transcriptomes. In September 2014, diArk contains about 2600 eukaryotes with 6000 genome and transcriptome assemblies, of which 22% are not available via NCBI/ENA/DDBJ. Several indicators for the quality of the assemblies are provided to facilitate their comparison for selecting the most appropriate dataset for further studies. diArk has a user-friendly web interface with extensive options for filtering and browsing the sequenced eukaryotes.
Allows global pathogen surveillance using whole genome sequencing (WGS). Pathogenwatch is a database that provides access to species and taxonomy prediction for over 60,000 variants of bacteria, viruses, and fungi. Users can upload their own assemblies with metadata for analysis and comparison with the Pathogenwatch public assemblies. Some analysis features are also available to perform multilocus sequence typing (MLST) prediction and core genome MLST (cgMLST) for a part of the schemes.
Provides an identifier for set of sequences that comprise a specific version of a genome assembly. Assembly is an online resource that stores the names and identifiers for the sequences in each genome assembly and records the organization of the component sequences into scaffolds and chromosomes. This enables the Assembly database to report the assembly structure and to provide mappings between names, synonyms and identifiers for assemblies, chromosomes or scaffolds.