FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4383554057> ?p ?o ?g. }

• W4383554057 abstract "Abstract Background Accurate variant calls from whole genome sequencing (WGS) of Plasmodium falciparum infections are crucial in malaria population genomics. Here a falciparum variant calling pipeline based on GATK version 4 (GATK4) was optimized and applied to 6626 public Illumina WGS samples. Methods Control WGS and accurate PacBio assemblies of 10 laboratory strains were leveraged to optimize parameters that control the heterozygosity, local assembly region size, ploidy, mapping and base quality in both GATK HaplotypeCaller and GenotypeGVCFs. From these controls, a high-quality training dataset was generated to recalibrate the raw variant data. Results On current high-quality samples (read length = 250 bp, insert size = 405–524 bp), the optimized pipeline shows improved sensitivity (86.6 ± 1.7% for SNPs and 82.2 ± 5.9% for indels) compared to the default GATK4 pipeline (77.7 ± 1.3% for SNPs; and 73.1 ± 5.1% for indels, adjusted P < 0.001) and previous variant calling with GATK version 3 (GATK3, 70.3 ± 3.0% for SNPs and 59.7 ± 5.8% for indels, adjusted P < 0.001). Its sensitivity on simulated mixed infection samples (80.8 ± 6.1% for SNPs and 78.3 ± 5.1% for indels) was again improved relative to default GATK4 (68.8 ± 6.0% for SNPs and 38.9 ± 0.7% for indels, adjusted, adjusted P < 0.001). Precision was high and comparable across all pipelines on each type of data tested. The resulting combination of high-quality SNPs and indels increases the resolution of local population population structure detection in sub-Saharan Africa. Finally, increasing ploidy improves the detection of drug resistance mutations and estimation of complexity of infection. Conclusions Overall, this study provides an optimized falciparum GATK4 pipeline resource for variant calling which should help improve genomic studies of malaria." @default.
• W4383554057 created "2023-07-08" @default.
• W4383554057 creator A5004418767 @default.
• W4383554057 creator A5018491787 @default.
• W4383554057 creator A5054207126 @default.
• W4383554057 date "2023-07-07" @default.
• W4383554057 modified "2023-10-14" @default.
• W4383554057 title "An optimized GATK4 pipeline for Plasmodium falciparum whole genome sequencing variant calling and analysis" @default.
• W4383554057 cites W1967607927 @default.
• W4383554057 cites W1969571661 @default.
• W4383554057 cites W1980752431 @default.
• W4383554057 cites W1984174967 @default.
• W4383554057 cites W2001102860 @default.
• W4383554057 cites W2010328983 @default.
• W4383554057 cites W2019851585 @default.
• W4383554057 cites W2027834647 @default.
• W4383554057 cites W2123284622 @default.
• W4383554057 cites W2124634096 @default.
• W4383554057 cites W2135697415 @default.
• W4383554057 cites W2140794408 @default.
• W4383554057 cites W2161311583 @default.
• W4383554057 cites W2166806965 @default.
• W4383554057 cites W2473686027 @default.
• W4383554057 cites W2514285416 @default.
• W4383554057 cites W2562857250 @default.
• W4383554057 cites W2581965723 @default.
• W4383554057 cites W2770095154 @default.
• W4383554057 cites W2779975541 @default.
• W4383554057 cites W2801980266 @default.
• W4383554057 cites W2969271119 @default.
• W4383554057 cites W2986984498 @default.
• W4383554057 doi "https://doi.org/10.1186/s12936-023-04632-0" @default.
• W4383554057 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/37420214" @default.
• W4383554057 hasPublicationYear "2023" @default.
• W4383554057 type Work @default.
• W4383554057 citedByCount "0" @default.
• W4383554057 crossrefType "journal-article" @default.
• W4383554057 hasAuthorship W4383554057A5004418767 @default.
• W4383554057 hasAuthorship W4383554057A5018491787 @default.
• W4383554057 hasAuthorship W4383554057A5054207126 @default.
• W4383554057 hasBestOaLocation W43835540571 @default.
• W4383554057 hasConcept C104317684 @default.
• W4383554057 hasConcept C119054055 @default.
• W4383554057 hasConcept C135763542 @default.
• W4383554057 hasConcept C141231307 @default.
• W4383554057 hasConcept C153209595 @default.
• W4383554057 hasConcept C192953774 @default.
• W4383554057 hasConcept C24432333 @default.
• W4383554057 hasConcept C2908647359 @default.
• W4383554057 hasConcept C54355233 @default.
• W4383554057 hasConcept C70721500 @default.
• W4383554057 hasConcept C71924100 @default.
• W4383554057 hasConcept C86803240 @default.
• W4383554057 hasConcept C99454951 @default.
• W4383554057 hasConceptScore W4383554057C104317684 @default.
• W4383554057 hasConceptScore W4383554057C119054055 @default.
• W4383554057 hasConceptScore W4383554057C135763542 @default.
• W4383554057 hasConceptScore W4383554057C141231307 @default.
• W4383554057 hasConceptScore W4383554057C153209595 @default.
• W4383554057 hasConceptScore W4383554057C192953774 @default.
• W4383554057 hasConceptScore W4383554057C24432333 @default.
• W4383554057 hasConceptScore W4383554057C2908647359 @default.
• W4383554057 hasConceptScore W4383554057C54355233 @default.
• W4383554057 hasConceptScore W4383554057C70721500 @default.
• W4383554057 hasConceptScore W4383554057C71924100 @default.
• W4383554057 hasConceptScore W4383554057C86803240 @default.
• W4383554057 hasConceptScore W4383554057C99454951 @default.
• W4383554057 hasFunder F4320332161 @default.
• W4383554057 hasIssue "1" @default.
• W4383554057 hasLocation W43835540571 @default.
• W4383554057 hasLocation W43835540572 @default.
• W4383554057 hasLocation W43835540573 @default.
• W4383554057 hasOpenAccess W4383554057 @default.
• W4383554057 hasPrimaryLocation W43835540571 @default.
• W4383554057 hasRelatedWork W1965921640 @default.
• W4383554057 hasRelatedWork W1994038182 @default.
• W4383554057 hasRelatedWork W2027675659 @default.
• W4383554057 hasRelatedWork W2063985242 @default.
• W4383554057 hasRelatedWork W2108817379 @default.
• W4383554057 hasRelatedWork W2154453877 @default.
• W4383554057 hasRelatedWork W2917890190 @default.
• W4383554057 hasRelatedWork W3165753654 @default.
• W4383554057 hasRelatedWork W3180309927 @default.
• W4383554057 hasRelatedWork W4316190287 @default.
• W4383554057 hasVolume "22" @default.
• W4383554057 isParatext "false" @default.
• W4383554057 isRetracted "false" @default.
• W4383554057 workType "article" @default.