These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
3. Comprehensive evaluation and guidance of structural variation detection tools in chicken whole genome sequence data. Ma C; Shi X; Li X; Zhang YP; Peng MS BMC Genomics; 2024 Oct; 25(1):970. PubMed ID: 39415108 [TBL] [Abstract][Full Text] [Related]
4. svclassify: a method to establish benchmark structural variant calls. Parikh H; Mohiyuddin M; Lam HY; Iyer H; Chen D; Pratt M; Bartha G; Spies N; Losert W; Zook JM; Salit M BMC Genomics; 2016 Jan; 17():64. PubMed ID: 26772178 [TBL] [Abstract][Full Text] [Related]
5. A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark. Pei Y; Tanguy M; Giess A; Dixit A; Wilson LC; Gibbons RJ; Twigg SRF; Elgar G; Wilkie AOM Genes (Basel); 2024 Jul; 15(7):. PubMed ID: 39062704 [TBL] [Abstract][Full Text] [Related]
6. VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing. Luo C; Liu YH; Zhou XM Nat Commun; 2024 Aug; 15(1):6956. PubMed ID: 39138168 [TBL] [Abstract][Full Text] [Related]
7. Comparison of structural variant callers for massive whole-genome sequence data. Joe S; Park JL; Kim J; Kim S; Park JH; Yeo MK; Lee D; Yang JO; Kim SY BMC Genomics; 2024 Mar; 25(1):318. PubMed ID: 38549092 [TBL] [Abstract][Full Text] [Related]
8. Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing. Kosugi S; Momozawa Y; Liu X; Terao C; Kubo M; Kamatani Y Genome Biol; 2019 Jun; 20(1):117. PubMed ID: 31159850 [TBL] [Abstract][Full Text] [Related]
9. Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. Zhao X; Collins RL; Lee WP; Weber AM; Jun Y; Zhu Q; Weisburd B; Huang Y; Audano PA; Wang H; Walker M; Lowther C; Fu J; ; Gerstein MB; Devine SE; Marschall T; Korbel JO; Eichler EE; Chaisson MJP; Lee C; Mills RE; Brand H; Talkowski ME Am J Hum Genet; 2021 May; 108(5):919-928. PubMed ID: 33789087 [TBL] [Abstract][Full Text] [Related]
10. iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data. Mimori T; Nariai N; Kojima K; Takahashi M; Ono A; Sato Y; Yamaguchi-Kabata Y; Nagasaki M BMC Syst Biol; 2013; 7 Suppl 6(Suppl 6):S8. PubMed ID: 24564972 [TBL] [Abstract][Full Text] [Related]
11. Benchmarking long-read aligners and SV callers for structural variation detection in Oxford nanopore sequencing data. Helal AA; Saad BT; Saad MT; Mosaad GS; Aboshanab KM Sci Rep; 2024 Mar; 14(1):6160. PubMed ID: 38486064 [TBL] [Abstract][Full Text] [Related]
12. Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software. Cameron DL; Di Stefano L; Papenfuss AT Nat Commun; 2019 Jul; 10(1):3240. PubMed ID: 31324872 [TBL] [Abstract][Full Text] [Related]
13. A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application. Grant JR; Herman EK; Barlow LD; Miglior F; Schenkel FS; Baes CF; Stothard P BMC Genomics; 2024 Sep; 25(1):903. PubMed ID: 39350025 [TBL] [Abstract][Full Text] [Related]
14. Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. Hall MB; Wick RR; Judd LM; Nguyen AN; Steinig EJ; Xie O; Davies M; Seemann T; Stinear TP; Coin L Elife; 2024 Oct; 13():. PubMed ID: 39388235 [TBL] [Abstract][Full Text] [Related]
15. SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines. Leung WY; Marschall T; Paudel Y; Falquet L; Mei H; Schönhuth A; Maoz Moss TY BMC Genomics; 2015 Mar; 16(1):238. PubMed ID: 25887570 [TBL] [Abstract][Full Text] [Related]
16. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Chaisson MJP; Sanders AD; Zhao X; Malhotra A; Porubsky D; Rausch T; Gardner EJ; Rodriguez OL; Guo L; Collins RL; Fan X; Wen J; Handsaker RE; Fairley S; Kronenberg ZN; Kong X; Hormozdiari F; Lee D; Wenger AM; Hastie AR; Antaki D; Anantharaman T; Audano PA; Brand H; Cantsilieris S; Cao H; Cerveira E; Chen C; Chen X; Chin CS; Chong Z; Chuang NT; Lambert CC; Church DM; Clarke L; Farrell A; Flores J; Galeev T; Gorkin DU; Gujral M; Guryev V; Heaton WH; Korlach J; Kumar S; Kwon JY; Lam ET; Lee JE; Lee J; Lee WP; Lee SP; Li S; Marks P; Viaud-Martinez K; Meiers S; Munson KM; Navarro FCP; Nelson BJ; Nodzak C; Noor A; Kyriazopoulou-Panagiotopoulou S; Pang AWC; Qiu Y; Rosanio G; Ryan M; Stütz A; Spierings DCJ; Ward A; Welch AE; Xiao M; Xu W; Zhang C; Zhu Q; Zheng-Bradley X; Lowy E; Yakneen S; McCarroll S; Jun G; Ding L; Koh CL; Ren B; Flicek P; Chen K; Gerstein MB; Kwok PY; Lansdorp PM; Marth GT; Sebat J; Shi X; Bashir A; Ye K; Devine SE; Talkowski ME; Mills RE; Marschall T; Korbel JO; Eichler EE; Lee C Nat Commun; 2019 Apr; 10(1):1784. PubMed ID: 30992455 [TBL] [Abstract][Full Text] [Related]
17. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. Linderman MD; Paudyal C; Shakeel M; Kelley W; Bashir A; Gelb BD Gigascience; 2021 Jul; 10(7):. PubMed ID: 34195837 [TBL] [Abstract][Full Text] [Related]
18. StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants. Sharo AG; Hu Z; Sunyaev SR; Brenner SE Am J Hum Genet; 2022 Feb; 109(2):195-209. PubMed ID: 35032432 [TBL] [Abstract][Full Text] [Related]
19. Parliament2: Accurate structural variant calling at scale. Zarate S; Carroll A; Mahmoud M; Krasheninina O; Jun G; Salerno WJ; Schatz MC; Boerwinkle E; Gibbs RA; Sedlazeck FJ Gigascience; 2020 Dec; 9(12):. PubMed ID: 33347570 [TBL] [Abstract][Full Text] [Related]
20. nanotatoR: a tool for enhanced annotation of genomic structural variants. Bhattacharya S; Barseghyan H; Délot EC; Vilain E BMC Genomics; 2021 Jan; 22(1):10. PubMed ID: 33407088 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]