Matthijs G, Souche E, Alders M, Corveleyn A, Eck S, Feenstra I, et al. Guidelines for diagnostic next-generation sequencing. Eur J Hum Genet. 2016;24:2–5.

Article  CAS  PubMed  Google Scholar 

Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol. 2021;82:801–11.

Article  CAS  PubMed  Google Scholar 

Johnson S, Lee K, Riccitelli N. A comparison of Illumina and Element Biosciences sequencing platforms. Cancer Res. 2024;327(6_Supplement):327.

Article  Google Scholar 

Kumar KR, Cowley MJ, Davis RL. Next-generation sequencing and emerging technologies. Semin Thromb Hemost. 2019;45:661–73.

Article  CAS  PubMed  Google Scholar 

Pedersen BS, Collins RL, Talkowski ME, Quinlan AR. Indexcov: fast coverage quality control for whole-genome sequencing. Gigascience. 2017;6:1–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. 2010.

Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal. 2011;17:10–2.

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen S, Huang T, Zhou Y, Han Y, Xu M, Gu J. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinform. 2017;18(Suppl 3):80.

Article  Google Scholar 

Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.

Article  PubMed  PubMed Central  Google Scholar 

Zverinova S, Guryev V. Variant calling: Considerations, practices, and developments. Hum Mutat. 2022;43:976–85.

Article  PubMed  Google Scholar 

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinform. 2013;43:1–33.

Google Scholar 

Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics. 2014;30:2843–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Koboldt DC. Best practices for variant calling in clinical sequencing. Genome Med. 2020;12:91.

Article  PubMed  PubMed Central  Google Scholar 

Donato L, Scimone C, Rinaldi C, D’Angelo R, Sidoti A. New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies. Neural Comput Appl. 2021;33:15669–92.

Article  PubMed  PubMed Central  Google Scholar 

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vasimuddin M, Sanchit M, Li H, Srinivas A. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS). 2019.

Jung Y, Han D. BWA-MEME: BWA-MEM emulated with a machine learning approach. Bioinformatics. 2022;38:2404–13.

Article  CAS  PubMed  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.

Article  PubMed  PubMed Central  Google Scholar 

Tischler G, Leonard S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol Med. 2014;9:13.

Article  PubMed Central  Google Scholar 

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, der Auwera GAV, et al. Scaling accurate genetic variant discovery to tens of thousands of samples. bioRxiv. 2018;10:201178.

Google Scholar 

Barbitoff YA, Abasov R, Tvorogova VE, Glotov AS, Predeus AV. Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery. BMC Genomics. 2022;23:155.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haile S, Corbett RD, Bilobram S, Bye MH, Kirk H, Pandoh P, et al. Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples. Nucleic Acids Res. 2019;47:e12.

Article  PubMed  Google Scholar 

Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res. 2013;41:e67.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tanaka N, Takahara A, Hagio T, Nishiko R, Kanayama J, Gotoh O, et al. Sequencing artifacts derived from a library preparation method using enzymatic fragmentation. PLoS ONE. 2020;15:e0227427.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang K, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, et al. Pathogenic germline variants in 10,389 adult cancers. Cell. 2018;173:355-370.e14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Highnam G, Wang JJ, Kusler D, Zook J, Vijayan V, Leibovich N, et al. An analytical framework for optimizing variant discovery from personal genomes. Nat Commun. 2015;6:6275.

Article  CAS  PubMed  Google Scholar 

Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP. igvjs: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics. 2023;39:btac830.

Article  CAS  PubMed  Google Scholar 

Yi D, Nam J-W, Jeong H. Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches. Brief Bioinform. 2023;24:bbad297.

Article  PubMed  PubMed Central  Google Scholar 

Whitford W, Lehnert K, Snell RG, Jacobsen JC. Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data. J Biomed Inform. 2019;94:103174.

Article  PubMed  Google Scholar 

Gabrielaite M, Torp MH, Rasmussen MS, Andreu-Sánchez S, Vieira FG, Pedersen CB, et al. A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data. Cancers. 2021;13:6283.

Article  CAS  PubMed  PubMed Central