From 1a4ae6b6bcba0eac28421eef35bd4ae933bea126 Mon Sep 17 00:00:00 2001
From: Bernardo Aguzzoli Heberle
 <81333350+bernardo-heberle@users.noreply.github.com>
Date: Fri, 22 Mar 2024 07:34:47 -0400
Subject: [PATCH] Update CITATIONS.md

---
 CITATIONS.md | 28 +++++-----------------------
 1 file changed, 5 insertions(+), 23 deletions(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index 5720817..eb26648 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -1,45 +1,35 @@
 # Citations
 
+
 ## Main
 
 [Nextflow](https://www.nextflow.io/docs/latest/index.html)
 
 [Singularity](https://docs.sylabs.io/guides/latest/user-guide/)
 
+
 ## Basecalling
 
 [pod5](https://pypi.org/project/pod5/)
 
 [dorado](https://github.com/nanoporetech/dorado)
 
-## Pre-processing
-
-[Pychopper](https://github.com/epi2me-labs/pychopper)
-
-[Porechop_ABI](https://github.com/bonsai-team/Porechop_ABI)
-
 
 ## Quality Control
 
 [PycoQC](https://github.com/a-slide/pycoQC)
 
-[RSeQC](https://rseqc.sourceforge.net/)
-
 [MultiQC](https://multiqc.info/)
 
 
-## Mapping
+## Alignment
 
 [Minimap2](https://github.com/lh3/minimap2)
 
 
-## Transcriptomics
-
-[GFFread](https://github.com/gpertea/gffread)
+## Methylation Calling
 
-[GFFcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml)
-
-[Bambu](https://github.com/GoekeLab/bambu)
+[Modkit](https://github.com/nanoporetech/modkit)
 
 
 ## Other Genomics Tools
@@ -47,14 +37,6 @@
 [Samtools](https://github.com/samtools/samtools)
 
 
-## R Packages
-
-[BioConductor](https://www.bioconductor.org/)
-
-[Bambu](https://github.com/GoekeLab/bambu)
-
-
-
 ## Other
 
 [Conda](https://docs.conda.io/en/latest/)
-- 
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