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Advanced computational methods in analyzing high-throughput sequencing data

Award Number: R01HG010040
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 05/01/2018
PERIOD OF PERFORMANCE END DATE: 02/28/2027

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Advanced computational methods in analyzing high-throughput sequencing data - PROJECT SUMMARY High-performance computational algorithms are essential to the analysis of large-scale biological sequence data and have received broad attention. Developed several years or even more than a decade ago, many mainstream software packages for sequence alignment, assembly and genome annotation do not take full advantage of modern accurate long-read data or cannot keep up with the throughput of current technologies. The development of advanced algorithms is critical to the applications of sequencing technologies in the near future. Based on our work in the previous funding cycle, this project will address this pressing need with four proposals: (1) developing an alignment algorithm for accurate long reads and high-quality assemblies for more comprehensive alignment through highly repetitive regions and long segmental duplications; (2) extending our hifiasm assembler to the high-quality assembly of more accurate Oxford Nanopore reads available nowadays; (3) combining our hifiasm and dipasm algorithms for more accurate and more contiguous haplotype-resolved assembly without pedigree data; (4) developing a protein-to-genome aligner to assist large-scale gene annotation of new species. Upon completion, the proposed studies will result in high-performance user facing tools for sequence alignment and assembly that are faster and more accurate than the current generation.


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: 2026 ( Subtotal = $436,100 )
2026	2026	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Human Genome Research	000	10	3/2/2026	NON-COMPETING CONTINUATION	$436,100
														Subtotal = $436,100

Issue Date FY: 2025 ( Subtotal = $436,100 )
2025	2025	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Human Genome Research	000	9	2/28/2025	NON-COMPETING CONTINUATION	$392,490
2025	2025	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Human Genome Research	001	9	4/28/2025	NON-COMPETING CONTINUATION	$43,610
														Subtotal = $436,100

Issue Date FY: 2024 ( Subtotal = $436,100 )
2024	2024	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Human Genome Research	001	8	5/25/2024	NON-COMPETING CONTINUATION	$35,600
2024	2024	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02215	SUFFOLK	USA	Human Genome Research	000	8	2/20/2024	NON-COMPETING CONTINUATION	$400,500
														Subtotal = $436,100

Issue Date FY: 2023 ( Subtotal = $445,000 )
2023	2023	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	7	2/24/2023	NON-COMPETING CONTINUATION	$445,000
														Subtotal = $445,000

Issue Date FY: 2022 ( Subtotal = $344,300 )
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	003	6	6/10/2022	COMPETING CONTINUATION	$175,334
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	001	6	6/7/2022	COMPETING CONTINUATION	$34,430
2022	2022	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	6	2/1/2022	COMPETING CONTINUATION	$309,870
2022	2021	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	002	5	6/10/2022	NON-COMPETING CONTINUATION	-$175,334
														Subtotal = $344,300

Issue Date FY: 2021 ( Subtotal = $397,125 )
2021	2021	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	5	3/11/2021	NON-COMPETING CONTINUATION	$397,125
														Subtotal = $397,125

Issue Date FY: 2020 ( Subtotal = $397,125 )
2020	2020	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	4	2/24/2020	NON-COMPETING CONTINUATION	$397,125
														Subtotal = $397,125

Issue Date FY: 2019 ( Subtotal = $404,893 )
2019	2019	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	002	3	2/12/2019	NON-COMPETING CONTINUATION	$397,125
2019	2018	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	005	1	4/30/2019	NEW	-$2
2019	2018	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	006	2	4/30/2019	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$2
2019	2018	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	003	1	4/16/2019	NEW	$26,456
2019	2018	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	1	1/14/2019	NEW	-$267,964
2019	2018	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	004	2	4/16/2019	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	-$12,241
2019	2018	DANA-FARBER CANCER INSTITUTE, INC.	450 BROOKLINE AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	001	2	1/15/2019	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$261,517
														Subtotal = $404,893

Issue Date FY: 2018 ( Subtotal = $400,500 )
2018	2018	BROAD INSTITUTE, INC., THE	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Human Genome Research	000	1	5/1/2018	NEW	$400,500
														Subtotal = $400,500

Grand Total All Awards = $3,697,243

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Advanced computational methods in analyzing high-throughput sequencing data

Award Number: R01HG010040

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 05/01/2018

PERIOD OF PERFORMANCE END DATE: 02/28/2027

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