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This article focuses on "how to assemble chloroplast genomes using GetOrganelle software". Interested friends may wish to take a look. The method introduced in this paper is simple, fast and practical. Let the editor take you to learn how to assemble chloroplast genomes using GetOrganelle software.

At present, the chloroplast genomes of plants are basically made directly from fresh leaves, the total DNA is extracted and sequenced, the second generation sequencing library is constructed, and then the chloroplast genome is assembled with ready-made software, eliminating the step of extracting chloroplasts.

There are many software for assembling chloroplast genomes using total DNA sequencing data, and there is a review of these tools.

Https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02153-6

I use GetOrganelle for this tweet today. The Github link of the software is https://github.com/Kinggerm/GetOrganelle.

The corresponding paper

Https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02154-5

The github home page of the software introduces in detail how to use the software. The software was developed by a teacher of Kunming Botanical Institute, and a QQ group is set up to answer questions. The qq group number can be seen at the end of the gitbub home page.

It is very easy to install using conda directly.

Conda install-c bioconda getorganelle

If you want to use the conda command on the linux system, you need to install miniconda or Anaconda3. I have previously recorded a video introducing the installation of Anaconda3 on the linux system. If you are not familiar with it, you can take a look at https://www.bilibili.com/video/BV1Ft4y1e7w2.

After the software is installed, you have to download the reference genome and run the following command

The command used for assembly is get_organelle_from_reads.py, and the parameters used are

-1-2 determine the path of double-ended sequencing data respectively.

-O define the file name of the output file

-R-k what exactly means I do not know,-R according to the help document directly set 15 should be OK,-k followed by the number can also be set according to his help document, now double-ended sequencing is usually 150bp, this-k parameter directly set 105and 121can, this number is less, the speed should be faster.

-F specifies the reference. If it is a chloroplast genome, it can be followed by embplant_pt directly.

Because of the high copy number of chloroplast genome, 2G of data is basically enough to assemble a complete genome. Therefore, it is enough to directly use the head command to get the first 20 million lines of genome sequencing data.

Head-n 20000000 data_R1.fastq > R1.fastq

Head-n 20000000 data_R2.fastq > R2.fastq

And finally, assembly.

Get_organelle_from_reads.py-1 R1.fastq-2 R2.fq-o plastome_output-R 15-k 105121-F embplant_pt

If the assembly is successful, we will eventually get two sequences, which are different in the direction of the small single copy region. My own way of processing is to select some related reference chloroplast genomes to construct the evolutionary tree and remove the one whose branch is obviously too long.

At this point, I believe you have a deeper understanding of "how to assemble chloroplast genomes using GetOrganelle software". You might as well do it in practice. Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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