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Algorithms and Software for the Assembly of Metagenomic Data

Award Number: R01AI100947
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 03/21/2013
PERIOD OF PERFORMANCE END DATE: 08/31/2029

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Algorithms and Software for the Assembly of Metagenomic Data - Project Summary The importance of the microbial communities inhabiting the human body cannot be understated, and currently, metagenomic sequencing is one of the primary ways through which these communities are being analyzed. While targeted assays exist, it is now widely accepted tha the analysis of the entire complement of genes found within the microbiome (which can only be obtained through metagenomic sequencing) is critical for understanding the role these microbes play in health and disease. An important analysis is metagenomic assembly—the process used to stitch together sequencing reads into contiguous DNA sequences (contigs) and metagenome-assembled genomes (MAGs). The reconstruction of full genomes can enable analyses of the strain structure of communities, association of antibiotic resistance or virulence genes with specific members of the community; and more. Thus, there is strong interest in the broader microbiome community in methods able to extract high-quality MAGs from metagenomic data. New technologies have made it easier to construct MAGs, however, significant challenges remain, particularly for low abundance organisms and when handling genomic variation between bacterial strains. This proposal will tackle such challenges, as follows. New assembly merging/reconciliation techniques will allow the integration of data across different sequencing technologies and metagenomic samples, thereby improving the recovery of the genomes of low abundance organisms. Such organisms are believed to play an important role in defining the community structure and through their impact on human health. A valuable tool for mining microbiome data sets is the identification of genomic segments shared across multiple samples, thus allowing their association with clinical parameters and distinguishing them from transient members of the microbiota. This project will develop new techniques for the discovery of conserved sequences, relying on statistical analyses of k-mers and graph analyses to improve accuracy while maintaining computational speed. The project will also address the fact that the genomes found in the samples may harbor a different combination of genes from the pangenome of a species than represented in any one of the reference genomes. Proposed is a new approach for using pangenome graphs to guide the assembly process, thus enabling the assembly process to automatically mix and match between the genomic content of the reference collection, while also improving efficiency by removing redundancy. Finally, this project proposes a novel graph-based paradigm for the discovery of bacteriophages—viruses that infect bacteria and that play an important role in defining the structure of microbial communities. Phages are also being considered a promising avenue for anti-bacterial therapies as we face increased rates of antimicrobial resistance. The approaches developed in this project will be implemented in usable and open-source software tools, allowing both academic and industrial reuse, and the data generated will be made publicly available.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $2,764,928 )
2025	2025	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BUILDING	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	001	9	9/4/2025	COMPETING CONTINUATION	$2,764,928
2025	2023	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BUILDING	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	8	4/15/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $2,764,928

Issue Date FY: 2023 ( Subtotal = $652,623 )
2023	2023	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	8	11/17/2022	NON-COMPETING CONTINUATION	$652,623
														Subtotal = $652,623

Issue Date FY: 2022 ( Subtotal = $702,991 )
2022	2022	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	7	11/19/2021	NON-COMPETING CONTINUATION	$702,991
														Subtotal = $702,991

Issue Date FY: 2021 ( Subtotal = $653,789 )
2021	2021	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	6	11/16/2020	NON-COMPETING CONTINUATION	$653,789
														Subtotal = $653,789

Issue Date FY: 2020 ( Subtotal = $634,665 )
2020	2020	UNIVERSITY OF MARYLAND	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	5	11/29/2019	COMPETING CONTINUATION	$634,665
														Subtotal = $634,665

Issue Date FY: 2018 ( Subtotal = $0 )
2018	2016	UNIVERSITY OF MARYLAND	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	4	6/19/2018	EXTENSION WITH OR WITHOUT FUNDS	$0
														Subtotal = $0

Issue Date FY: 2016 ( Subtotal = $531,911 )
2016	2016	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	4	2/11/2016	EXTENSION WITH OR WITHOUT FUNDS	$531,911
														Subtotal = $531,911

Issue Date FY: 2015 ( Subtotal = $545,209 )
2015	2015	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	3	2/10/2015	NON-COMPETING CONTINUATION	$545,209
														Subtotal = $545,209

Issue Date FY: 2014 ( Subtotal = $435,034 )
2014	2014	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	2	2/17/2014	NON-COMPETING CONTINUATION	$435,034
														Subtotal = $435,034

Issue Date FY: 2013 ( Subtotal = $437,391 )
2013	2013	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	001	1	6/10/2013	NEW	$18,613
2013	2013	UNIVERSITY OF MARYLAND	4101 CHESAPEAKE BLDG	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Allergy and Infectious Diseases Research	000	1	3/21/2013	NEW	$418,778
														Subtotal = $437,391

Grand Total All Awards = $7,358,541

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Algorithms and Software for the Assembly of Metagenomic Data

Award Number: R01AI100947

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 03/21/2013

PERIOD OF PERFORMANCE END DATE: 08/31/2029

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