https://github.com/broadinstitute/blend_seq_paper
A repository to hold code used for the Blend Seq paper
Science Score: 36.0%
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Found 1 DOI reference(s) in README -
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Links to: biorxiv.org -
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Low similarity (6.9%) to scientific vocabulary
Repository
A repository to hold code used for the Blend Seq paper
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: bsd-3-clause
- Language: WDL
- Default Branch: main
- Size: 16 MB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Blend-Seq Paper
This repository contains the code used in the paper:
- Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery
A copy of the preprint can be found here. A summary will appear as a poster at AGBT 2025. Please refer to the paper for more details on the methods and results.
Data
The GATK-SV VCF used in the paper for a short-read control can be found under data. It comes from the following paper:
Zan Koenig, Mary T Yohannes, Lethukuthula L Nkambule, and others. A harmonized public
resource of deeply sequenced diverse human genomes. Genome Research, 2024
Code Overview
The code is split into scripts and pipelines. For documentation on what they do and how they were used, please see the Methods section of the manuscript.
External Code
The following external code was used in the paper: * BenchmarkSVs for benchmarking structural variants * BenchmarkVCFs.wdl for benchmarking small variants * chop_reads for chopping long read alignments into synthetic short read alignments * CleanSVs.wdl for cleaning SV VCFs to normalize for downstream tools
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
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