An effective graph-based toolkit to assembly plant organelle genomes into simple and accurate master graphs, consisting of many graph-based tools for processing the genome assembly results and high throughout sequencing data.
Just download the file and uncompress it to where you want to install in. The executable file gsat could be found in the bin directory.
#install by using git
git clone https://github.com/hwc2021/GSAT.git
cd GSAT/bin
chmod a+x gsat
#install by downloading the source codes
#put the source code file "GSAT-main.zip" where you want to install in
unzip GSAT-main.zip
cd GSAT-main/bin
chmod a+x gsat
Edit the .bashrc file to add this directory to your environment variable PATH. For example, in a typical Linux system:
vi ~/.bashrc
#add the next line to the end of .bashrc file ("#" should be removed when paste the next line to the file)
#export PATH=$PATH:/your/path/GSAT/bin
source ~/.bashrc
This toolkit required several necessary tools which should be installed in the PATH:
- blastn
- minimap2 (version >= 2.19)
- mafft
- SPAdes [used only in graphShort pipeline]
gsat <command> [options]
Commands:
-- Functions
graphFilt filter the assembly graph with different params
graphMap conduct graph mapping to detect mapped paths in a graph for query sequence
graphCorr correct the sequences in a graph by using long reads. HIFI reads is recommanded.
graphSimplify simplify the graph based on supported mapped paths of long reads.
rmOverlap remove the overlaping regions from a graph
-- Pipelines
graphShort generate a Organelle Graph from a raw graph of de novo assembly
graphLong generate a Mitochondrial Rough Graph from a OG
graphSimplification generate a Mitochondrial Rough Master Graph from a MRG
graphCorrection generate a Mitochondrial Master Graph from a MRMG
-- Information
help print a brief help information
man print a complete help document
version print the version information
Detailed usage information for each command could be found by using the command without any option.
All pipeline commands can be easily applied with a specified configure file, which provides all necessary params to the pipelines of GSAT. The detailed params for each pipeline can be found in the example configure file example.conf. Notably, each pipeline reads only valid options from the configure file, i.e., params for different pipelines can be either put together in a single configure file or put in different files.
-
graphShort
gsat graphShort -conf example.conf
This will generate a raw graph of de novo genome assembly based on Illumina paired-end reads, and then produce a Organelle Graph (OG). The OG will be saved as og.filtered.gfa in the output dir. Please note that the params for graphShort should be adjusted for different species, so the resulted OG should be checked and edited in Bandage before it can be used for the next pipeline.
-
graphLong
gsat graphLong -conf example.conf
This will generate a Mitochondrial Rough Graph (MRG) from a OG based on graph-mapping between OG and long reads. The MRG will be saved as mrg.filtered.gfa in the output dir.
-
graphSimplification
gsat graphSimplification -conf example.conf
This will generate a Mitochondrial Rough Master Graph (MRMG) from a MRG. The MRMG will be saved as mrmg.simplified.gfa in the output dir.
-
graphCorrection
gsat graphCorrection -conf example.conf
This will generate a Mitochondrial Master Graph (MMG) from a MRMG. The MMG will be saved as mmg.corrCtg.gfa in the output dir.
GSAT version 1.12 (2024-04-30)
Wenchuang He nongke2@163.com / hewenchuang@caas.cn AGIS, CAAS
He, W., Xiang, K., Chen, C., Wang, J., and Wu, Z. (2023). Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework. Brief Bioinform 2410.1093/bib/bbac522.
Any comments, bug reports, and suggestions are very welcomed. They will help us to further improve GSAT. If you have any troubles running GSAT, please leave your comments and bug reports at our GitHub issues page or sent it via e-mail.