contera

Contera - a tool to detect and delete non-target organisms and adapters contamination in your genome assembly. Contera Uses BLAST against NT and custom adapters databases to find contaminations.

Dependencies

Contera is written and tested on python >= 3.5. To run it you should install BLAST NT database on your system (~ 110GB)

Install

To install contera with Conda use following command:

conda create -c contera_env -c zilov contera

And than activate the environment: conda activate contera_env

Download or set BLAST NT database

If you do not have database in your system, you can download it with following command (Please make sure that you have 120 Gb of free space!):

contera -m download_db -o /path/to/outdir

If you already have database in your system, please add CONTERA_DB in your PATH with the following command (Make sure tha database was build with makeblastdb!):

export CONTERA_BLAST=/path/to/blast_db_folder/nt

Usage

Contera has three modes to run:

1. Contamination - to check for contamination with BLAST NT database and delete it from your genome assembly, to run it use:

   contera -m cont -a /path/to/assembly.fasta -db /path/to/blast_db -o /path/to/outdir

2. Adapters - to check for contamination with adapters database, to run it use:

   contera -m adapter -a /path/to/assembly.fasta -o /path/to/outdir

3. All-in-one (default) - to check for both adapters and other organisms contaminations, to run it use:

   contera -a /path/to/assembly.fasta -db /path/to/blast_db -o /path/to/outdir

Options

  -h, --help            show this help message and exit
  -m {aio, cont, adapter, download_db}, --mode {aio, cont, adapter, download_db}
                        mode to use [default = aio]
  -a ASSEMBLY, --assembly ASSEMBLY
                        path to genome assembly in FASTA format
  -p PREFIX, --prefix PREFIX
                        prefix for output files
  -l LENGTH, --length LENGTH
                        length threshold to delete short contigs
  -o OUTDIR, --outdir OUTDIR
                        output directory
  -db BLAST_DB, --blast_db BLAST_DB
                        path to blast nucleotide (nt) database
  -t THREADS, --threads THREADS
                        number of threads [default == 8]
  -d, --debug           do not run, print commands only