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Methods for sequencing data analysis and archive-scale data science

Award Number: R35GM139602
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 01/01/2021
PERIOD OF PERFORMANCE END DATE: 12/31/2025

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Methods for sequencing data analysis and archive-scale data science - PROJECT SUMMARY We will develop methods and maintain software that make it radically easier for biomedical researchers to use and understand sequencing data. The project will support our maintaining and improving our popular “upstream” tools for analyzing sequencing data. These include the Bowtie and Bowtie 2 tools for read alignment, the Kraken 2 tool for metagenomics classiﬁcation and the Dashing tool for genomic sketching and comparison. We will also develop new systems that allow researchers to use these same core tools (Bowtie, Kraken 2, Dashing) to rapidly discover and vet archived datasets. We will enable researchers to quickly ascertain whether a dataset is of high quality, what species are present, whether contaminants are present, what assay was performed, what datasets are similar to each other, and what datasets are inconsistent with annotated metadata. In this way, researchers can distill relevant archived datasets, those having the expected biological properties, in a way that does not hinge on the accuracy of the associated metadata. Finally, we will work to develop new infrastructure for large-scale reanalysis and indexing of archived data, ultimately yielding new “search engines” for scientiﬁc question-answering. In particular, we will extend our past work on the Rail-RNA, recount2 and Snaptron so that we can more effectively analyze huge collections of archived data, converting them into a variety of useful summary forms, and than adding a layer of indexing so that users can query the summaries in the context of a scientiﬁc investigation. We will also create new catalogs and mechanisms whereby researchers can share their archive-assisted study designs, so that useful combinations of archived datasets, and insights into where their metadata might be incorrect or incomplete, can be reported and shared.


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 = $462,653 )
2025	2025	THE JOHNS HOPKINS UNIVERSITY	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	001	5	12/17/2024	NON-COMPETING CONTINUATION	$462,653
2025	2024	THE JOHNS HOPKINS UNIVERSITY	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	000	4	11/4/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $462,653

Issue Date FY: 2024 ( Subtotal = $514,058 )
2024	2024	THE JOHNS HOPKINS UNIVERSITY	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	001	4	6/20/2024	NON-COMPETING CONTINUATION	$51,405
2024	2024	THE JOHNS HOPKINS UNIVERSITY	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	000	4	12/18/2023	NON-COMPETING CONTINUATION	$462,653
														Subtotal = $514,058

Issue Date FY: 2023 ( Subtotal = $514,058 )
2023	2023	JOHNS HOPKINS UNIVERSITY, THE	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	001	3	2/27/2023	NON-COMPETING CONTINUATION	$51,405
2023	2023	JOHNS HOPKINS UNIVERSITY, THE	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	000	3	12/23/2022	NON-COMPETING CONTINUATION	$462,653
														Subtotal = $514,058

Issue Date FY: 2022 ( Subtotal = $514,058 )
2022	2022	JOHNS HOPKINS UNIVERSITY, THE	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	000	2	1/7/2022	NON-COMPETING CONTINUATION	$462,652
2022	2022	JOHNS HOPKINS UNIVERSITY, THE	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	001	2	6/30/2022	NON-COMPETING CONTINUATION	$51,406
														Subtotal = $514,058

Issue Date FY: 2021 ( Subtotal = $414,787 )
2021	2021	JOHNS HOPKINS UNIVERSITY, THE	3400 N CHARLES ST	BALTIMORE	MD	21218	BALTIMORE CITY	USA	Biomedical Research and Research Training	000	1	12/29/2020	NEW	$414,787
														Subtotal = $414,787

Grand Total All Awards = $2,419,614

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Methods for sequencing data analysis and archive-scale data science

Award Number: R35GM139602

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 01/01/2021

PERIOD OF PERFORMANCE END DATE: 12/31/2025

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