Supporting files generated during the genome project of Baronia brevicornis from "The genome of the short-horned baronia (Baronia brevicornis), an endangered relict and key lineage in swallowtail butterfly evolution"

These files are part of the manuscript:The genome of the short-horned baronia (Baronia brevicornis), an endangered relict and key lineage in swallowtail butterfly evolutionAlba Marino 1,†, Eliette L. Reboud 1†, Emmanuelle Chevalier 1, Marie-Ka Tilak 1, Jorge Contreras-Garduño 2, Benoit Nabholz 1,3† and Fabien L. Condamine 1,*†1 Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France2 Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico3 Institut Universitaire de France (IUF), Paris, France† These authors contributed equally.Genome assembly is available here : https://www.ncbi.nlm.nih.gov/nuccore/JASFAT000000000.1/Files descriptions: Baronia_brevicornis_FC897_final_version.fasta_masked.fasta : Masked genome assemblyBaronia_brevicornis_FC897_braker2.gtf : GTF file of the annotation performed with BRAKER2 pipelineBaronia_brevicornis_FC897_braker2.codingseq.fasta : CDS of the annotation performed with BRAKER2 pipelineBaronia_brevicornis_FC897_braker2.proteins.fasta : Proteins of the annotation performed with BRAKER2 pipelineBaronia_brevicornis_FC897_rnd3.all.maker.noseq.gff : GFF3 file of the annotation performed with MAKER pipelineBaronia_brevicornis_FC897_rnd3.all.maker.proteins.fasta : Proteins of the annotation performed with MAKER pipelineBaronia_brevicornis_FC897_rnd3.all.maker.transcripts.fasta : CDS of the annotation performed with MAKER pipelinecreateMaskFile.py is a python script to create mask files for MSMC2. Usage : python3 createMaskFile.py coverage_file.txt 15 100 contig_name output.bed.gz. The coverage_file.txt is create using "samtools depth" program.AlgnRM2Fasta : is a program to extract the alignment of TE sequences with their sequence consensus from RepeatMaskerNucleodite_diversity_coding_sequences_scripts.zip : Script and program compute the synonymous, non-synonymous and four-fold degenerated sites nucleotide diversity

本数据集文件隶属于以下研究手稿：《短角凤蝶（Baronia brevicornis）的基因组——一种濒危孑遗类群，亦是凤蝶演化中的关键支系》
作者列表：Alba Marino¹,†、Eliette L. Reboud¹†、Emmanuelle Chevalier¹、Marie-Ka Tilak¹、Jorge Contreras-Garduño²、Benoit Nabholz¹,3† 与 Fabien L. Condamine¹,*
¹ 蒙彼利埃进化科学研究所（蒙彼利埃大学 | 法国国家科学研究中心（CNRS） | 法国发展研究院（IRD） | 法国高等研究应用学院（EPHE）），法国蒙彼利埃，欧仁·巴塔永广场，34095
² 墨西哥国立自治大学国立高级研究学院莫雷利亚校区，墨西哥米却肯州莫雷利亚，安提瓜帕茨夸罗公路#8701，圣何塞德拉韦尔塔前庄园社区，58190
³ 法国大学研究所（IUF），法国巴黎
† 共同第一作者
* 通讯作者
基因组组装数据可通过以下链接获取：https://www.ncbi.nlm.nih.gov/nuccore/JASFAT000000000.1/

文件说明如下：
1. Baronia_brevicornis_FC897_final_version.fasta_masked.fasta：经序列屏蔽的基因组组装文件（masked genome assembly）
2. Baronia_brevicornis_FC897_braker2.gtf：基于BRAKER2注释流程得到的基因转移格式（GTF）文件
3. Baronia_brevicornis_FC897_braker2.codingseq.fasta：基于BRAKER2注释流程得到的编码序列（CDS）文件
4. Baronia_brevicornis_FC897_braker2.proteins.fasta：基于BRAKER2注释流程得到的蛋白质序列文件
5. Baronia_brevicornis_FC897_rnd3.all.maker.noseq.gff：基于MAKER注释流程得到的通用特征格式3（GFF3）文件
6. Baronia_brevicornis_FC897_rnd3.all.maker.proteins.fasta：基于MAKER注释流程得到的蛋白质序列文件
7. Baronia_brevicornis_FC897_rnd3.all.maker.transcripts.fasta：基于MAKER注释流程得到的编码序列（CDS）文件

附属工具与脚本说明：
1. createMaskFile.py：用于为MSMC2软件生成屏蔽文件的Python脚本。使用方法：python3 createMaskFile.py coverage_file.txt 15 100 contig_name output.bed.gz。其中coverage_file.txt可通过samtools depth工具生成。
2. AlgnRM2Fasta：用于从重复序列屏蔽工具（RepeatMasker）的结果中提取转座因子（TE）序列与其序列共识联配结果的程序。
3. Nucleodite_diversity_coding_sequences_scripts.zip：用于计算同义突变位点、非同义突变位点及四价简并位点核苷酸多样性的脚本与程序包。