[TOC]

PFGI

introduce

PFGI is a bioinformatics pipeline for fungal genome identification and annotation.

How to use the tool

1. Download: clone from github: git clone https://github.com/lyotvincent/PFGI.git
2. 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.
3. Download fungal genomes & build database. python download_fungi_data.py. Next, the database path should be written in the configuration file.
4. 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

External tools

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