FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2891874253> ?p ?o ?g. }

• W2891874253 abstract "Abstract Illumina sequencing has revolutionized yeast genomics, with prices for commercial draft genome sequencing now below $200. The popular SPAdes assembler makes it simple to generate a de novo genome assembly for any yeast species. However, whereas making genome assemblies has become routine, understanding what they contain is still challenging. Here, we show how graphing the information that SPAdes provides about the length and coverage of each scaffold can be used to investigate the nature of an assembly, and to diagnose possible problems. Scaffolds derived from mitochondrial DNA, ribosomal DNA, and yeast plasmids can be identified by their high coverage. Contaminating data, such as cross-contamination from other samples in a multiplex sequencing run, can be identified by its low coverage. Scaffolds derived from the bacteriophage PhiX174 and Lambda DNAs that are frequently used as molecular standards in Illumina protocols can also be detected. Assemblies of yeast genomes with high heterozygosity, such as interspecies hybrids, often contain two types of scaffold: regions of the genome where the two alleles assembled into two separate scaffolds and each has a coverage level C , and regions where the two alleles co-assembled (collapsed) into a single scaffold that has a coverage level 2 C . Visualizing the data with Coverage-versus-Length (CVL) plots, which can be done using Microsoft Excel or Google Sheets, provides a simple method to understand the structure of a genome assembly and detect aberrant scaffolds or contigs. We provide a Python script that allows assemblies to be filtered to remove contaminants identified in CVL plots. 100-word article summary We describe a simple new method, Coverage-versus-Length plots, for examining de novo genome sequence assemblies. These plots enable researchers to detect scaffolds that have unusually high or unusually low coverage, which allows contaminants, and scaffolds that come from atypical parts of the organism’s DNA complement, to be detected. We show that contaminants are common in yeast genomes sequenced in multiplex Illumina runs. We provide instructions for making plots using Microsoft Excel or Google Sheets, and software for filtering assemblies to remove contaminants. Contaminants can be detected and removed, even without knowing their source." @default.
• W2891874253 created "2018-09-27" @default.
• W2891874253 creator A5012728257 @default.
• W2891874253 creator A5022811442 @default.
• W2891874253 creator A5040066540 @default.
• W2891874253 creator A5047306799 @default.
• W2891874253 creator A5055296320 @default.
• W2891874253 creator A5065500580 @default.
• W2891874253 creator A5079361647 @default.
• W2891874253 creator A5080526729 @default.
• W2891874253 date "2018-09-19" @default.
• W2891874253 modified "2023-09-25" @default.
• W2891874253 title "Coverage-versus-Length plots, a simple quality control step for de novo yeast genome sequence assemblies" @default.
• W2891874253 cites W1502636502 @default.
• W2891874253 cites W1923694921 @default.
• W2891874253 cites W1990456795 @default.
• W2891874253 cites W2016376064 @default.
• W2891874253 cites W2120902911 @default.
• W2891874253 cites W2336459044 @default.
• W2891874253 cites W2344852138 @default.
• W2891874253 cites W2475920490 @default.
• W2891874253 cites W2528315574 @default.
• W2891874253 cites W2547473733 @default.
• W2891874253 cites W2623597117 @default.
• W2891874253 cites W2765746097 @default.
• W2891874253 cites W2782546270 @default.
• W2891874253 cites W2793409442 @default.
• W2891874253 cites W2809850832 @default.
• W2891874253 cites W2883782133 @default.
• W2891874253 cites W2886981252 @default.
• W2891874253 doi "https://doi.org/10.1101/421347" @default.
• W2891874253 hasPublicationYear "2018" @default.
• W2891874253 type Work @default.
• W2891874253 sameAs 2891874253 @default.
• W2891874253 citedByCount "0" @default.
• W2891874253 crossrefType "posted-content" @default.
• W2891874253 hasAuthorship W2891874253A5012728257 @default.
• W2891874253 hasAuthorship W2891874253A5022811442 @default.
• W2891874253 hasAuthorship W2891874253A5040066540 @default.
• W2891874253 hasAuthorship W2891874253A5047306799 @default.
• W2891874253 hasAuthorship W2891874253A5055296320 @default.
• W2891874253 hasAuthorship W2891874253A5065500580 @default.
• W2891874253 hasAuthorship W2891874253A5079361647 @default.
• W2891874253 hasAuthorship W2891874253A5080526729 @default.
• W2891874253 hasBestOaLocation W28918742531 @default.
• W2891874253 hasConcept C104317684 @default.
• W2891874253 hasConcept C113425843 @default.
• W2891874253 hasConcept C141231307 @default.
• W2891874253 hasConcept C150194340 @default.
• W2891874253 hasConcept C162317418 @default.
• W2891874253 hasConcept C18949551 @default.
• W2891874253 hasConcept C192953774 @default.
• W2891874253 hasConcept C2781188995 @default.
• W2891874253 hasConcept C54355233 @default.
• W2891874253 hasConcept C59582021 @default.
• W2891874253 hasConcept C70721500 @default.
• W2891874253 hasConcept C86803240 @default.
• W2891874253 hasConceptScore W2891874253C104317684 @default.
• W2891874253 hasConceptScore W2891874253C113425843 @default.
• W2891874253 hasConceptScore W2891874253C141231307 @default.
• W2891874253 hasConceptScore W2891874253C150194340 @default.
• W2891874253 hasConceptScore W2891874253C162317418 @default.
• W2891874253 hasConceptScore W2891874253C18949551 @default.
• W2891874253 hasConceptScore W2891874253C192953774 @default.
• W2891874253 hasConceptScore W2891874253C2781188995 @default.
• W2891874253 hasConceptScore W2891874253C54355233 @default.
• W2891874253 hasConceptScore W2891874253C59582021 @default.
• W2891874253 hasConceptScore W2891874253C70721500 @default.
• W2891874253 hasConceptScore W2891874253C86803240 @default.
• W2891874253 hasLocation W28918742531 @default.
• W2891874253 hasLocation W28918742532 @default.
• W2891874253 hasLocation W28918742533 @default.
• W2891874253 hasOpenAccess W2891874253 @default.
• W2891874253 hasPrimaryLocation W28918742531 @default.
• W2891874253 hasRelatedWork W1632541129 @default.
• W2891874253 hasRelatedWork W2119433654 @default.
• W2891874253 hasRelatedWork W2155471120 @default.
• W2891874253 hasRelatedWork W2170482852 @default.
• W2891874253 hasRelatedWork W2291614554 @default.
• W2891874253 hasRelatedWork W2517624897 @default.
• W2891874253 hasRelatedWork W2779945812 @default.
• W2891874253 hasRelatedWork W2890379969 @default.
• W2891874253 hasRelatedWork W2891300676 @default.
• W2891874253 hasRelatedWork W2949294873 @default.
• W2891874253 isParatext "false" @default.
• W2891874253 isRetracted "false" @default.
• W2891874253 magId "2891874253" @default.
• W2891874253 workType "article" @default.