LAPIS is a fast web API for massive open virus sequencing databases (preprint)

Via a web API, we make large open pathogen genome sequencing datasets available for real-time interactive analysis. Developed for SARS-CoV-2 and recently extended to monkeypox, the Lightweight API for Sequences (LAPIS) enables complex mutation and metadata queries and aggregations on massive datasets from GenBank at unprecedented speed. LAPIS is accompanied by our own dashboards on genspectrum.org aiming to support evidence-based public health responses.

[1]  N. Magini,et al.  Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages , 2022, medRxiv.

[2]  Shivashankar H. Nagaraj,et al.  Unlocking capacities of genomics for the COVID-19 response and future pandemics , 2022, Nature Methods.

[3]  Alaa Abdel Latif,et al.  Outbreak.info Research Library: A standardized, searchable platform to discover and explore COVID-19 resources , 2022, bioRxiv.

[4]  T. Stadler,et al.  CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants , 2021, Bioinform..

[5]  M. Kraemer,et al.  Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa , 2021, Nature.

[6]  G. Gao,et al.  The emergence, genomic diversity and global spread of SARS-CoV-2 , 2021, Nature.

[7]  Timothy M. Sykes,et al.  Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland , 2021, Epidemics.

[8]  R. Lanfear,et al.  Want to track pandemic variants faster? Fix the bioinformatics bottleneck , 2021, Nature.

[9]  R. Neher,et al.  Nextclade: clade assignment, mutation calling and quality control for viral genomes , 2021, J. Open Source Softw..

[10]  Trevor Bedford,et al.  Ten recommendations for supporting open pathogen genomic analysis in public health , 2020, Nature Medicine.

[11]  Murray S. Kucherawy,et al.  Zstandard Compression and the application/zstd Media Type , 2018, RFC.

[12]  Trevor Bedford,et al.  Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.