A bioinformatics tool designed to enable rapid recovery of high-quality draft genomes of microbial eukaryotes from various environmental metagenomic samples.
- reference-independent and cultivation-free
- separate reads or contigs into five groups: Bacteria, Archaeal, Eukaryotic, Viral, and Unknown.
- generate a fasta file with Euk and unknown contigs for binning
Schematic representation of Eukfinder workflows. Eukfinder is a taxonomic classification-based bioinformatics approach to retrieve microbial eukaryotic nuclear and mitochondrial genomes from WGS metagenomic sequencing data. Eukfinder has two different workflows based on the input files, (a) Eukfinder_short using Illumina short reads, it first classifies Illumina reads into 5 distinct taxonomic categories (Archaeal, Bacterial, Viral, Eukaryotic, and Unknown), after assembling the Eukaryotic and Unknown reads together, second round of classification and supervised binning, it will output Eukaryotic nuclear and mitochondrial genomes, and (b) Eukfinder_long using MAG assembled contigs or long-read sequencing data generated by Nanopore or Pacbio platforms. It goes through one round of classification to select Eukaryotic and Unknown contigs, and after supervised binning generates Eukaryotic nuclear and mitochondrial genomes.
spades, seqkit, trimmomatic, bowtie2, centrifuge, acc2tax, plast
Python >= 3.7
ete3, numpy, pandas, joblib, pyqt, bs4, dask, urllib3, multiprocessing, distributed
A step-by-step tutorial on installation.
Note: We are working to making Eukfinder available on Bioconda, so that this tutorial may be frequently updated.
git clone https://github.com/RogerLab/Eukfinder.gitPlease install conda first.
conda env create -f eukfindertest.yml
# activate it
source activate eukfindertest(Required) Install PLAST
wget https://github.com/PLAST-software/plast-library/releases/download/v2.3.2/plastbinary_linux_v2.3.2.tar.gz
tar -zxf plastbinary_linux_v2.3.2.tar.gz
export PATH=/path/to/plastbinary_linux_v2.3.2/bin:$PATH(Required) Install acc2tax
https://github.com/richardmleggett/acc2tax
(Required for supervised binning) Install MyCC
https://sourceforge.net/projects/sb2nhri/files/MyCC/
Default reference databases can be downloaded from Eukfinder Databases
- Plast Database
- Centrifuge Database
- acc2tax Database
Users can flexibly customize the reference data (see here)
See Wiki for detailed description
Eukfinder read_prep Run Trimmomatic to remove low-quality reads, and adaptors Run Bowtie2 to remove host reads Run Centrifuge for the first round of classification
Eukfinder read_prep [-h] --r1 R1 --r2 R2 -n THREADS -i ILLUMINA_CLIP
--hcrop HCROP -l LEADING_TRIM -t TRAIL_TRIM --wsize
WSIZE --qscore QSCORE --mlen MLEN --hg HG -o
OUT_NAME --cdb CDB
Eukfinder short_seqs
Eukfinder short_seqs [-h] --r1 R1 --r2 R2 --un UN -o OUT_NAME -n
NUMBER_OF_THREADS -z NUMBER_OF_CHUNKS -t
TAXONOMY_UPDATE -p PLAST_DATABASE -m PLAST_ID_MAP
[-p2 ANCILLARY_PLAST_DATABASE]
[-m2 ANCILLARY_PLAST_ID_MAP]
[--force-pdb FORCE_PDB] -a ACC2TAX_DATABASE --cdb
CDB -e E_VALUE --pid PID --cov COV --max_m MAX_M
--mhlen MHLEN --pclass PCLASS --uclass UCLASS
Eukfinder long_seqs
Eukfinder long_seqs [-h] -l LONG_SEQS -o OUT_NAME --mhlen MHLEN --cdb
CDB -n NUMBER_OF_THREADS -z NUMBER_OF_CHUNKS -t
TAXONOMY_UPDATE -p PLAST_DATABASE -m PLAST_ID_MAP
-a ACC2TAX_DATABASE -e E_VALUE --pid PID --cov COV
Contributions are what makes the open-source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.
If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!
Distributed under the MIT License. See LICENSE.txt for more information.
## Publication/Citation Zhao, D., Salas-Leiva, D.E., Williams, S.K., Dunn, K.A. and Roger, A.J., 2023. Eukfinder: a pipeline to retrieve microbial eukaryote genomes from metagenomic sequencing data. bioRxiv, pp.2023-12.
## Contact d.zhao@dal.ca