binner runs multipe metagenome binning programs using a single command.
Currently binner supports these metagenome binning programs:
CONCOCT: https://github.com/BinPro/CONCOCT
MaxBin2: https://sourceforge.net/projects/maxbin2/
MetaBat: https://bitbucket.org/berkeleylab/metabat/src/master/
blobtools: https://github.com/DRL/blobtools
- MacOS X or other Unix like operating system A container runtime:
- Docker: https://www.docker.com/get-started or
- Singularity/Apptainer: https://apptainer.org/
Assuming Docker is installed and configured properly, it is straightforward to install binner:
$ git clone git clone https://github.com/reslp/binner.git
$ cd binner
$ chmod +x binner
$ ./binner -h
Welcome to binner. A script to quickly run metagenomic binning software using Docker.
Usage: binner [-v] [-a <assembly_file>] [-f <read_file1>] [-r <read_file2>] [-m maxbin,metabat,blobtools,concoct] [-t nthreads] [[--diamonddb=/path/to/diamonddb --protid=/path/to/prot.accession2taxid]] [-q] [-b [--buscosets=set1,set2]]
Options:
-a <assembly_file> Assembly file in FASTA format
-f <read_file1> Forward read file in FASTQ format (can be gzipped)
-r <read_file2> Reverse read file in FASTQ format (can be gzipped)
IMPORTANT: Currently the assembly and read files need to be in the same directory which has to the directory in which binner is run.
-m <maxbin,metabat,blobtools,concoct> specify binning software to run.
Seperate multiple options by a , (eg. -m maxbin,blobtools).
-t number of threads for multi-threaded parts
-q run QUAST on the binned sets of contigs
-b run BUSCO on the binned sets of contigs. See additional details below.
--multiqc Run multiqc after all binning steps to create a summary report on all the bins. This should be used together with -q, -b or both.
-v Display program version
Options specific to blobtools:
The blobtools container used here uses diamond instead of blast to increase speed.
Options needed when blobtools should be run. The blobtools container used here uses diamond instead of blast to increase speed.
--diamonddb= full (absolute) path to diamond database
--protid= full (absolute) path to prot.accession2taxid file provided by NCBI
Options needed when BUSCO analysis of contigs should be performed:
The blobtools container used here uses diamond instead of blast to increase speed.
Options needed when blobtools should be run. The blobtools container used here uses diamond instead of blast to increase speed.
--buscosets= BUSCO sets which should be tested. This will be run for each set of contigs. Individual sets should be comma
separated. eg. --buscosets=fungi_odb9,bacteria_odb9,insects_odb9 .
Running this assumes that folders with the busco sets exist in the current working directory. They should have
the same name as passed to the --buscosets command. If they are not found binner will try to download them
from the BUSCO website.
binner can run multiple binning programs. The components of different binners are contained as individual Docker containers. It is not necessary to install them individually. Most metagenomic binners need an assembly and the associated read files used to create the assembly. Binner expects that the Assembly to filter is provided in FASTA format and the read files in FASTQ format. binner creates output in the directory it is executed in.
Additionally binner can perform downstream analyses to evaluate (with BUSCO and QUAST) and aggregate (with multiqc) binning results.
Running MetaBat with binner:
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m metabat
Running MaxBin with binner:
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m maxbin
Running CONCOCT with binner:
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m concoct
Running blobtools with binner:
Blobtools requires blast results to get the taxonomic identity (by using NCBI taxids) of individual contigs in the assembly. binner creates these blast results with diamond blastx. However you will need a diamond based sequence database (typically the NCBI nr database). If you don't already have one you can set it up like this.
$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
$ docker run --rm reslp/diamond diamond makedb --in nr.gz -d nr
Using this command has the advantage that the database is compatible with the used diamond Docker container used in binner which is reslp/binner.
Because diamond cannot output taxids directly binner maps the ids retrieved by diamond blastx to NCBI taxids. This is done using the file prot.accession2taxid provided by NCBI. If you don't have this file already download by running the following commands:
$ wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
$ gunzip prot.accession2taxid.gz
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m blobtools -b /path/to/diamonddb -p /path/to/prot.accession2taxid
Run multiple binners
binner can also run multiple binners in one go:
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m metabat,maxbin,concoct,blobtools -b /path/to/diamonddb -p /path/to/prot.accession2taxid
Analyze bins with QUAST and BUSCO
It is possible to analyze the created bins with QUAST and BUSCO directly with binner to identify interesting sets of bins. Output for this will be produced in the directory containing the bins.
This can be done with two commandline flags -q for quast and -bfor busco. Here are some example commands:
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m concoct -q
This command will run concoct to create bins and QUAST to evaluate the individual bins.
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m maxbin -b --buscosets=fungi_odb9,dikarya_odb9
The above command will run maxbin to identify bins of contigs and will run the specified BUSCO analyses --buscosets=fungi_odb9,dikarya_odb9 on each set of bins. Names of the used busco sets should refer to the names on the BUSCO website. The folders for each BUSCO set should be placed in the working directory. If they are not found, binner will try to download them directly from the BUSCO website.
Aggregate results with multiqc
To include multiqc into your binner run use a command like this:
$ binner -a metagenome.fasta -f forward_readfile.fq -r reverse_readfile.fq -m maxbin,blobtools,concoct -b -q --buscosets=fungi_odb9,dikarya_odb9 -b /path/to/diamonddb -p /path/to/prot.accession2taxid --multiqc
This command will run binning with maxbin,blobtools and concoct and perform downstream analyses with BUSCO and QUAST and will aggregate results with multiqc.
Copyright (C) 2019-2023 Philipp Resl
binner is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
binner is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program in the file LICENSE. If not, see http://www.gnu.org/licenses/.