WGDdetector: a pipeline for whole genome duplication (WGD) detecting with the genome or transcriptome annotations. Our paper has been published at BMC Bioinformatics:
"Yang Y, Li Y, Chen Q, Sun Y, Lu Z: WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations. BMC Bioinformatics 2019, 20(1):75."
We have updated the pipeline and using some more fast software or method to reduce the time wasting. The new pipeline also including 4 steps:
Software requirements (all path of the needed software should be list in this file WGDdetector_path/config/software.config)
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perl >5.0, including the perl moudule of threads and Bioperl
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python 2.7
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R >= 3.5
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parallel
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mmseqs2
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blast >= ncbi-blast-2.2.28+
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BlastGraphMetrics (https://github.com/trgibbons/BlastGraphMetrics)
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mcl
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muscle
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fastme
This pipline is a series perl scripts, you can just replace those scripts' header with the right perl path.
cd WGDdetector_path
perl setup.pl
cd example
sh 00.run.sh
The dS dsitribution results of different software and datasets descripted in the WGDdetector parper (https://github.com/yongzhiyang2012/WGDdetector_paper_results).
wgddetector (v1.00)
Usage: wgddetector --input_cds <cds_file> --input_pep <pep_file> --output_dir <output_dir> --tmp_dir <tmp_dir> --thread_num <thread_num> --cluster_engine <blastp|mmseqs2>
Options:
--input_cds input CDS in fasta format
--input_pep input protein in fasta format
--output_dir the output dir, which containing the main results
--tmp_dir the tmp dir
--thread_num the thread number when runnig this script
--cluster_engine "blastp" or "mmseqs2". when setted this as mmseqs2, the protein aligning and clustering will be faster than blast
--clean "yes" or "no". If selected yes, the tmp_dir will removed after finish. Default: yes
--run_cluster "yes" or "no". If selected yes, the protein blast and mcl clustering will generate. If selected no, the clustering file "output_dir/01.cluster/all-protein-clustering.result" must be existed
** The sequence IDs within the CDS and protein files must be same!