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PFGI is a bioinformatics pipeline for fungal genome identification and annotation.
- Download: clone from github: git clone https://github.com/lyotvincent/PFGI.git
- Configuration file: User could set software parameters in pfgi_configuration_template.xlsx and use "-conf_file_path pfgi_configuration.xlsx" to let program know where the configuration file is.
- Download fungal genomes & build database.
python download_fungi_data.py. Next, the database path should be written in the configuration file. - run this command to get 'help': python fungi_pipeline.py -h
help information:
-f #input single end file (fastq format)
-1 and -2 #input paired end files (fastq format)
-ngs or -3gs #choose which mode to run (Required)
-conf_file_path #the configuration file path (Required)
-o #out directory name
-h or -help or --h or --help #get help information
a example:
python ../PFGI/fungi_pipeline.py -1 SRR7530142_1.fastq -2 SRR7530142_2.fastq -ngs -conf_file_path ../PFGI/pfgi_configuration_template.xlsx -o SRR7530142
These software/tools respectively support part of the entire pipeline. If you want to use all the functions of the pipeline, all these software in the table should be installed.
The ✔ in 'conda' column means that the software cound install by conda.
| software | conda | download link |
|---|---|---|
| FastQC | ✔ | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| fastp | ✔ | https://github.com/OpenGene/fastp |
| trimmomatic | ✔ | https://github.com/timflutre/trimmomatic |
| cutadapt | ✔ | https://github.com/marcelm/cutadapt |
| sickle-trim | ✔ | https://github.com/najoshi/sickle |
| megahit | ✔ | https://github.com/voutcn/megahit |
| spades | ✔ | https://github.com/ablab/spades |
| velvet | ✔ | https://github.com/dzerbino/velvet |
| canu | ✔ | https://github.com/marbl/canu |
| QUAST | ✔ | https://github.com/ablab/quast |
| BLAST | ✔ | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| prokka | ✔ | https://github.com/tseemann/prokka |
| snap-aligner | ✔ | https://github.com/amplab/snap |
| bowtie2 | ✔ | https://github.com/BenLangmead/bowtie2 |
| samtools | ✔ | https://github.com/samtools/samtools |
| minimap2 | ✔ | https://github.com/lh3/minimap2 |
| biopython | ✔ | pip |
| bcbio-gff | ✔ | pip |
| datasketch | × | pip |
| xlrd | ✔ | pip |
| pyyaml | ✔ | pip |
| mlst | ✔ | https://github.com/tseemann/mlst |
An example for installing these software :
conda install -y fastqc