From 4fb212f2485af8ac136bf95e2bd1d4ac858490d8 Mon Sep 17 00:00:00 2001
From: Shihab Dider <shihabdider@gmail.com>
Date: Fri, 12 Jan 2024 08:18:51 -0500
Subject: [PATCH] Add choo 2023 citation

---
 README.md | 26 +++++++++++++++++---------
 1 file changed, 17 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 2fc7c90..acf121e 100644
--- a/README.md
+++ b/README.md
@@ -21,6 +21,23 @@
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/mskilab-org/nf-jabba)
 
+## Citations
+
+An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
+
+> **Most large structural variants in cancer genomes can be detected without long reads.**
+> Choo, ZN., Behr, J.M., Deshpande, A. et al.
+>
+> _Nat Genet_ 2023 Nov 09. doi: [https://doi.org/10.1038/s41588-023-01540-6](https://doi.org/10.1038/s41588-023-01540-6)
+>
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+
 ## Introduction
 
 **mskilab-org/nf-JaBbA** is a new state-of-the-art bioinformatics pipeline from [`mskilab-org`](https://www.mskilab.org/) for running [`JaBbA`](https://github.com/mskilab-org/JaBbA/tree/master), our algorithm for doing MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data. This pipeline runs all the pre-requisite modules and generates the necessary inputs for running JaBbA. It is designed to take tumor-normal pairs of human samples as input. 
@@ -162,14 +179,5 @@ We thank the following people for their extensive guidance in the development of
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-## Citations
-
-An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
 
-> **The nf-core framework for community-curated bioinformatics pipelines.**
->
-> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
->
-> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).