https://github.com/mskcc/ngs-stats
NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Times
https://github.com/mskcc/ngs-stats
Last synced: about 1 year ago
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NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Times
- Host: GitHub
- URL: https://github.com/mskcc/ngs-stats
- Owner: mskcc
- Created: 2019-02-19T16:40:24.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2025-06-09T14:41:58.000Z (about 1 year ago)
- Last Synced: 2025-06-17T23:06:29.023Z (about 1 year ago)
- Language: HTML
- Homepage:
- Size: 3.18 MB
- Stars: 1
- Watchers: 10
- Forks: 0
- Open Issues: 3
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Metadata Files:
- Readme: README.md
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README
A Java/SpringBoot, Tomcat & MySQL application initiated in 2018 originally running on delphi.mskcc.org (now igodb.mskcc.org) which has 17 tables with IGO (Integrated Genomics Operation) post sequencing information such as:
File name information for over 1.5 million fastq files written by IGO since 2011 in the table archivedfastq
Sequencer start-stop times in the table startstopsequencer so the lab can track sequencer availability.
10x Cell Ranger Stats in tables cellrangersummaryvdj and cellrangersummarycount.
Code to parse several Broad picard.jar output files and store in the database - HS Metrics, Duplication Metrics, Alignment Summary Metrics, RNA Seq Metrics & WGS Metrics, and crosscheckmetrics.
Picard naming conventions follow the Picard Metrics Definitions:
https://broadinstitute.github.io/picard/picard-metric-definitions.html
This project uses Lombok, to build with IntelliJ or Eclipse see:
https://www.baeldung.com/lombok-ide