ZGA - prokaryotic genome assembly and annotation pipeline

Installation

Installing dependencies

ZGA is written in Python and tested with Python 3.6 and Python 3.7. ZGA uses several software and libs including:

• fastqc
• ea-utils
• bbmap (or seqprep)
• spades
• unicycler
• CheckM
• DFast
• BioPython

All of them may be installed using conda:

It's highly recommended to create a new conda environment:

conda create -n newcoolenv python=3.7 fastqc ea-utils spades unicycler checkm-genome seqprep dfast bbmap blast biopython

and activate it

conda activate newcoolenv

Otherwise you may install dependencies to existing conda environment:

conda install python>=3.6 fastqc ea-utils spades unicycler checkm-genome seqprep dfast bbmap blast biopython

Of course, it's possible to use another ways even compile all tools from source code. In this case you should check if binaries are in your '$PATH' variable.

Get source from Github

You can get ZGA by cloning from the repository with git clone https://github.com/laxeye/zga.git or by downloading an archive.

Install from PyPi

Run pip install zga it will check if You have Biopython and istall it if not. But all other dependencies You should install manually or using conda. CheckM is available on PyPi, but it's easier to install it using conda.

Operating systems requirements

ZGA was tested on Ubuntu 18.04. Most probably any modern 64-bit Linux distribuition is enough.

Your feedback on other OS is welcome!

Usage

You should run zga.py if You cloned the source code or zga otherwise.

Run 'zga.py -h' to get a help message.

Examples:

Perform all steps (read qc, read trimming and merging, assembly, CheckM assesment with default (bacterial) marker set, DFAST annotation) and use 4 threads, where possible:

zga.py -1 R1.fastq.gz -2 R2.fastq.gz --threads 4 -o my_assembly

or use SPAdes and provide it with paired-end and nanopore reads of archaeal genome (Checfkm will use archaeal markers)

zga.py -1 R1.fastq.gz -2 R2.fastq.gz --nanopore MiniION.fastq.gz -a spades --threads 4 --domain archaea -o my_assembly

or from Nanopore reads only using unicycler

zga.py --nanopore MiniION.fastq.gz -o nanopore_assembly

Perform genome assesment and annotation:

With 'Pectobacterium' CheckM marker set:

zga.py --step check -g pectobacterium_sp.fasta --checkm_rank genus --checkm_taxon Pectobacterium -o my_output_dir

Let CheckM to infer the right marker set:

zga.py --step check -g my_genome.fa --checkm_mode lineage -o my_output_dir

Know issues and limitations

Don't forget: ZGA is in the early testing...

I hope to fix next issues ASAP:

• It's not posible to provide multiple read libraries i.e. tow sets of PE reads or two nanopore runs.
• It's not possible to install all dependencies with Python 3.8 via conda, please use 3.7 or 3.6.
• There is no conda package

Don't hesitate to report bug or feature!

Cite

It's a great pleasure to know, that your software is useful. Please cite ZAG:

Korzhenkov A. (2020). ZGA: prokaryotic genome assembly and annotation pipeline.

And of course tools it's using:

Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data.

Aronesty, E. (2015). ea-utils: Command-line tools for processing biological sequencing data. 2011. URL https://github. com/ExpressionAnalysis/ea-utils.

Bushnell, B., Rood, J., & Singer, E. (2017). BBMerge–accurate paired shotgun read merging via overlap. PloS one, 12(10).

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., ... & Pyshkin, A. V. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of computational biology, 19(5), 455-477.

Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017). Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS computational biology, 13(6), e1005595.

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome research, 25(7), 1043-1055.

Tanizawa, Y., Fujisawa, T., & Nakamura, Y. (2018). DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics, 34(6), 1037-1039.

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410.

Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., ... & De Hoon, M. J. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422-1423.