Pan-genome Graph Algorithms and Data Integration

Grant number: 872539

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Key facts

  • Disease

    COVID-19
  • Start & end year

    2020
    2023
  • Known Financial Commitments (USD)

    $1,235,884.18
  • Funder

    European Commission
  • Principal Investigator

    N/A

  • Research Location

    Italy
  • Lead Research Institution

    UNIVERSITA' DEGLI STUDI DI MILANO-BICOCCA
  • Research Priority Alignment

    N/A
  • Research Category

    Pathogen: natural history, transmission and diagnostics

  • Research Subcategory

    Pathogen genomics, mutations and adaptations

  • Special Interest Tags

    N/A

  • Study Type

    Non-Clinical

  • Clinical Trial Details

    N/A

  • Broad Policy Alignment

    Pending

  • Age Group

    Not Applicable

  • Vulnerable Population

    Not applicable

  • Occupations of Interest

    Not applicable

Abstract

Researchers involved in PANGAIA are investigating how massive amounts of genome sequence data can be ordered and analysed for their use in biomedicine. Their work has important implications in areas such as bacteria and virus research, investigation of drug resistance mechanisms and vaccine development: big data technology can help to identify the characteristics of new strains of viruses such as SARS-CoV-2 and bacteria by comparing their genomes.

Publicationslinked via Europe PMC

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View all publications at Europe PMC

MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.

Differential quantification of alternative splicing events on spliced pangenome graphs.

PangeBlocks: customized construction of pangenome graphs via maximal blocks.

Constructing and personalizing population pangenome graphs.

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.

ESKEMAP: exact sketch-based read mapping.

Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.

Hybrid-hybrid correction of errors in long reads with HERO.

Comparing methods for constructing and representing human pangenome graphs.