[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