A pipeline for the identification of fungi in public metagenomics datasets.
This version of the pipeline is used for running FindFungi on a single Unix server as opposed to a compute cluster/load sharing facility.
The FindFungi pipeline uses the metagenomics read-classifier Kraken with 32 custom fungal databases to generate 32 taxon predictions for a single read. These 32 predictions are combined to generate a consensus prediction. All reads are then BLASTed against their predicted genomes to generate read distribution skewness scores to select for the most likely true positives.
Download the pipeline, databases, associated scripts, prerequisites and other tools. Run the pipeline:
./FindFungi-0.23.3.sh /path/to/FASTQ-file.fastq Dataset-name
These instructions will hopefully allow you to get a copy of FindFungi up and running on your own server for development or your own analyses.
FindFungi v0.23 was built using the following:
- gcc version 4.4.4 20100726 (Red Hat 4.4.4-13)
- coreutils 8.27
- python 2.7.13 (modules: sys, os, ete3, Bio, math, argparse, itertools, collections, re)
- skewer 0.2.2
- kraken 0.10.5-beta
- ncbi blast 2.2.30
- Rscript 3.3.3 (packages: wordcloud)
- graphviz 2.40.1
- Download all of the scripts from GitHub/GiantSpaceRobot and move to a directory (/your/directory/scripts). You may need to give these scripts more permissions (e.g. chmod 755 *).
- In the FindFungi-v0.23.3 script, change the absolute paths of skewer, kraken, blast, the shell and python scripts to reflect your environment, or add these tools and scripts to you $PATH. You will also need to edit the LowestCommonAncestor.sh script to include the path to the downloaded scripts.
- Download the Kraken and BLAST databases from this website (http://bioinformatics.czc.hokudai.ac.jp/findfungi/).
- Uncompress these files and put them somewhere sensible:
tar -xvfz Kraken_*.tar.gz
mv Kraken_* Kraken_DB_Directory/
Download the dataset ERR675624 from the European Nucleotide Archive database. This dataset contains fungal reads.
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR675/ERR675624/ERR675624_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR675/ERR675624/ERR675624_2.fastq.gz
Gunzip these files and concatenate them, as we have no need to read pair information.
gunzip ERR675624_*.fastq.gz
cat ERR675624_*.fastq > ERR675624_both-pairs.fastq
Execute the FindFungi pipeline on this FASTQ file. We use nohup here to allow the pipeline to run in the background.
nohup ./FindFungi-0.23.sh /path/to/ERR675624_both-pairs.fastq ERR675624
The first command line argument (/path/to/ERR675624_both-pairs.fastq) points to your FASTQ file. The second (ERR675624) is the name FindFungi will use for this dataset. This name should be informative.
The .csv results should show the following:
#Taxon name,Taxid,Reads mapping to taxid,Reads mapping to children taxids,Pearson skewness score,Percent of pseudo-chromosomes with read hits
Candida sp. LDI48194,1759314,671,0,0.524623062587,100.0
Malassezia restricta,76775,378,0,0.496034792692,100.0
Candida tropicalis MYA-3404,294747,265,0,-0.265788716977,100.0
- Paul Donovan, PhD (email: pauldonovandonegal@gmail.com)
- Gabriel Gonzalez, PhD (e-mail: gagonzalez@czc.hokudai.ac.jp)
This project is licensed under the MIT License.