From 0ec4bbff48dff4f7d5e642d71f1e8037232e8e2d Mon Sep 17 00:00:00 2001
From: Arslan Tariq <arslan.tariq@hhu.de>
Date: Fri, 15 Nov 2024 15:13:16 +0100
Subject: [PATCH] add Readme file for assys

---
 assays/BUSCO_and_Compleasm_db/README.md       |   2 ++
 assays/BUSCO_and_Compleasm_db/isa.assay.xlsx  | Bin 7011 -> 7011 bytes
 assays/Genome_annotations/README.md           |   2 ++
 assays/Genome_annotations/isa.assay.xlsx      | Bin 12499 -> 12499 bytes
 assays/Genome_assemblies/README.md            |   4 ++++
 assays/Genome_assemblies/isa.assay.xlsx       | Bin 9952 -> 9952 bytes
 assays/Mercator_Bins/README.md                |   2 ++
 assays/Mercator_Bins/isa.assay.xlsx           | Bin 9746 -> 9746 bytes
 assays/Transposable_elements/README.md        |   2 ++
 assays/Transposable_elements/isa.assay.xlsx   | Bin 11931 -> 11931 bytes
 isa.investigation.xlsx                        | Bin 8325 -> 8325 bytes
 studies/Camellia_sinensis_pangenome/README.md |   6 +++---
 .../isa.study.xlsx                            | Bin 12983 -> 12983 bytes
 13 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/assays/BUSCO_and_Compleasm_db/README.md b/assays/BUSCO_and_Compleasm_db/README.md
index e69de29..4ed7623 100644
--- a/assays/BUSCO_and_Compleasm_db/README.md
+++ b/assays/BUSCO_and_Compleasm_db/README.md
@@ -0,0 +1,2 @@
+# Orthologs database
+These are the eudicots_odb10 databases that were used for the [BUSCO](https://busco.ezlab.org/) and [Compleasm](https://github.com/huangnengCSU/compleasm) analysis.
\ No newline at end of file
diff --git a/assays/BUSCO_and_Compleasm_db/isa.assay.xlsx b/assays/BUSCO_and_Compleasm_db/isa.assay.xlsx
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diff --git a/assays/Genome_annotations/README.md b/assays/Genome_annotations/README.md
index e69de29..55d32a7 100644
--- a/assays/Genome_annotations/README.md
+++ b/assays/Genome_annotations/README.md
@@ -0,0 +1,2 @@
+# Genome Annotations
+The combination of ab initio gene prediction using the deep learning tool  [Helixer](https://github.com/weberlab-hhu/Helixer) and the RNASeq-based [StringTie](https://ccb.jhu.edu/software/stringtie/) predicted transcripts were combined with a high-quality genome annotation with [Mikado](https://mikado.readthedocs.io/en/stable/) to select the best transcript sets.
\ No newline at end of file
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diff --git a/assays/Genome_assemblies/README.md b/assays/Genome_assemblies/README.md
index e69de29..74545f8 100644
--- a/assays/Genome_assemblies/README.md
+++ b/assays/Genome_assemblies/README.md
@@ -0,0 +1,4 @@
+# Genome assembly
+The genome of Anjibaicha, Zijuan, and L618 was initially assembled using [Hifiasm](https://www.nature.com/articles/s41592-020-01056-5) ([v0.19.5] and then purge the assembly using [Purge Haplotigs](https://bitbucket.org/mroachawri/purge_haplotigs/src/master/).
+We only had [Hi-C](https://en.wikipedia.org/wiki/Hi-C_(genomic_analysis_technique)) data for Anjibaicha. First, the Hi-C reads were processed using [Arima pipeline](https://github.com/ArimaGenomics/mapping_pipeline) and then removed small contigs which were highly similar to large scaffolds using [Purge Haplotigs](https://bitbucket.org/mroachawri/purge_haplotigs/src/master/).
+We didn't have Hi-C data for ZJ and L618, so we used [RagTag](https://github.com/malonge/RagTag) using the AJ chromosome as a reference.
\ No newline at end of file
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diff --git a/assays/Mercator_Bins/README.md b/assays/Mercator_Bins/README.md
index e69de29..5c06ae8 100644
--- a/assays/Mercator_Bins/README.md
+++ b/assays/Mercator_Bins/README.md
@@ -0,0 +1,2 @@
+# Functional annotation
+The functional annotation for all accession's proteome was performed using [Mercator4](https://www.plabipd.de/mercator_main.html)
\ No newline at end of file
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diff --git a/assays/Transposable_elements/README.md b/assays/Transposable_elements/README.md
index e69de29..f5eaaae 100644
--- a/assays/Transposable_elements/README.md
+++ b/assays/Transposable_elements/README.md
@@ -0,0 +1,2 @@
+# Transposable Elements (TEs) annotation
+The advanced Extensive de novo TE Annotator [EDTA](https://github.com/oushujun/EDTA) to identify TEs within the tea genomes. The LTR, TIR, and Helitron modes were run separately, followed by a final EDTA run with `-overwrite 0` and `--cds` options using Mikado's gene model CDS sequence, ensuring accurate and comprehensive annotation of TEs. For pan TE identification, the panEDTA module was used
\ No newline at end of file
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diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx
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diff --git a/studies/Camellia_sinensis_pangenome/README.md b/studies/Camellia_sinensis_pangenome/README.md
index 47423b6..5430713 100644
--- a/studies/Camellia_sinensis_pangenome/README.md
+++ b/studies/Camellia_sinensis_pangenome/README.md
@@ -1,3 +1,3 @@
-# *Camellia* genomes
-
-De novo genome assemblies of 3 diverse tea accessions, the purple-leaved *assamica* cultivar “Zijuan”, the temperature-sensitive *sinensis* cultivar “Anjibaicha” and the wild accession “L618” were merged with eight existing *Camellia* genomes to generate a new pan genome. To obtain leaf material for the de novo assemblies, plants were grown in the tea germplasm resource nursery of Huazhong Agricultural University, Wuhan, China.
+# *Camellia sinensis* genomes
+
+De novo genome assemblies of 3 diverse tea accessions, the purple-leaved *assamica* cultivar “Zijuan”, the temperature-sensitive *sinensis* cultivar “Anjibaicha” and the wild accession “L618” were merged with eight existing *Camellia* genomes to generate a new pan genome. To obtain leaf material for the de novo assemblies, plants were grown in the tea germplasm resource nursery of Huazhong Agricultural University, Wuhan, China.
diff --git a/studies/Camellia_sinensis_pangenome/isa.study.xlsx b/studies/Camellia_sinensis_pangenome/isa.study.xlsx
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-- 
GitLab