This repository was created by Xiaole Yin (xiaole99) and is currently maintained by Xi Chen (xinhec). The goal is to make args_oap faster, and easier to run.
If your OS satisfies all the dependencies (python>=3.7, diamond>=2.0.15, bwa>=0.7.17, blast>=2.12, samtools>=1.15), then build from source:
git clone https://github.com/xinehc/args_oap.git
cd args_oap
python setup.py install # use python3 if needed
Example
Two example fasta files (100k paired-end reads, 100 bp each) can be found here. The zipped file can be downloaded manually or using wget:
# conda install wget
wget https://dl.dropboxusercontent.com/s/pqgftlo24rfc2rd/example.tar.gz
tar -xvf example.tar.gz
cd example
# conda activate args_oap
args_oap stage_one -i input -o output -f fa -t 8
args_oap stage_two -i output -t 8
After stage_one, a metadata.txt file can be found in output. It summarizes the estimated 16S and cell copy numbers in each sample, for example:
sample
nRead
n16S
nCell
STAS
200000
8.229297879794053
3.1472376316269055
SWHAS104
200000
7.009547807125172
3.487830355315917
After stage_two, the normalized ARGs copies per 16S/cells or hits per million reads will be shown in several *_normalized_*.txt files.
For example, normalized_cell.type means:
normalized_cell - normalized against cell number
type - type of ARGs (the hierarchy in the SARG database is type -> subtype -> gene)
type
STAS
SWHAS104
aminoglycoside
0.04236519416057223
0.1411521328969608
bacitracin
0.03724412673456899
0.07331127852930945
beta_lactam
0.0
0.14920548807040623
macrolide-lincosamide-streptogramin
0.0
0.02404226144950743
multidrug
0.012948920209830746
0.19382414709324317
mupirocin
0.007757298735456341
0.009159215245515702
quinolone
0.37832158835366747
0.08842494718334318
sulfonamide
0.035174054192357015
0.1368367904789564
tetracycline
0.012183242185747383
0.09987284037027115
Output file extracted.filtered.fa contains all filtered ARG-like sequences after stage_two. blastout.filtered.txt is the metadata of these sequences.
De-contamination:
Before running ARGs-OAP, a de-contamination processes is recommended to secure clean prokaryotic reads. This includes the removal of genomic sequences from hosts (e.g., human), and from fungal sources. This step is critical to avoid potential biases in the calculation of cell numbers which relies on the identification of essential single copy marker genes.
Notes
(optional) Single/Paired end files
If you use paired-end files, please make sure the forward/reverse reads end with _1|_2, _R1|_R2 or _fwd|_rev (followed by .format, see -f, .gz optional), otherwise they will not be considered as a single sample. Example for fasta format files (-f fa):
To use customized databases (e.g. mobile genetic elements or heave metal resistant genes), you need to prepare two files:
nucleotide sequences or amino acid (protein) sequences database (e.g. database.fasta)
hierarchical structure file (e.g. structure.txt)
The database should be indexed manually (protein or nucleotide, in fasta):
## protein or nucleotide
args_oap make_db -i database.fasta
The structure file structure.txt should be tab-separated and the first column the sequences ID of database.fasta (please note that the sequence ID cannot contain space, tab and other irregular char such as forward slash). At lease one column (level 1) is required. For the one column (level 1) case, you may construct the structure file using:
Using ARG_OAP -> Upload Files module to upload the extracted fasta file and meta_data_online.txt file generated in stage one into Galaxy
Click ARG_OAP and Ublast_stagetwo, select your uploaded files
For "Column in Metadata:" chose the column you want to classify your samples (default: 3)
Click Execute and you can find four output files for your information
After a while or so, you will notice that their are four files generated for your information.
File 1 and 2: PcoA figures of your samples and other environment samples generated by ARGs abundance matrix normalization to 16S reads number and cell number File 3 and 4: Other tabular mother tables which including the profile of ARGs type and sub type information, as long as with other environment samples mother table. File3 results of ARGs abundance normalization against 16S reads number; File 4 results of ARGs abundance normalization against cell number
There are some questions raised by users, please refer to the FAQ for details. To run ARG OAP locally, users should download the source code into local computer system (Unix/Linux). Users can upload the generated files for stage two onto our Galaxy analysis platform (http://smile.hku.hk/SARGs) or use the local version of stage two script.
Notice:
This tools only provide the required scripts for ARGs-OAP 3.0 pipeline
This pipeline is distributed in the hope to achieve the aim of management of antibiotic resistant genes in environment, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.This pipeline is only allowed to be used for non-commercial and academic purpose.
The SARG database is distributed only freely used for academic purpose, any commercial use should require the agreement from the developer team.
ARGs_OAP
This repository was created by Xiaole Yin (xiaole99) and is currently maintained by Xi Chen (xinhec). The goal is to make args_oap faster, and easier to run.
If you have any questions, please create an issue, or contact Xiaole Yin (yinlele99@gmail.com).
More about the SARG database: https://smile.hku.hk/ARGs/Indexing, and the change logs: CHANGELOG.md.
Installation
Conda (macOS/Linux):
We suggest to create a new conda environment (here use
-n args_oapas an example) to avoid potential conflicts of dependencies:If your OS satisfies all the dependencies (
python>=3.7,diamond>=2.0.15,bwa>=0.7.17,blast>=2.12,samtools>=1.15), then build from source:Example
Two example fasta files (100k paired-end reads, 100 bp each) can be found here. The zipped file can be downloaded manually or using
wget:After
stage_one, ametadata.txtfile can be found inoutput. It summarizes the estimated 16S and cell copy numbers in each sample, for example:After
stage_two, the normalized ARGs copies per 16S/cells or hits per million reads will be shown in several*_normalized_*.txtfiles. For example,normalized_cell.typemeans:normalized_cell- normalized against cell numbertype- type of ARGs (the hierarchy in the SARG database is type -> subtype -> gene)Output file
extracted.filtered.facontains all filtered ARG-like sequences afterstage_two.blastout.filtered.txtis the metadata of these sequences.De-contamination:
Before running ARGs-OAP, a de-contamination processes is recommended to secure clean prokaryotic reads. This includes the removal of genomic sequences from hosts (e.g., human), and from fungal sources. This step is critical to avoid potential biases in the calculation of cell numbers which relies on the identification of essential single copy marker genes.
Notes
(optional) Single/Paired end files
If you use paired-end files, please make sure the forward/reverse reads end with
_1|_2,_R1|_R2or_fwd|_rev(followed by.format, see -f,.gzoptional), otherwise they will not be considered as a single sample. Example for fasta format files (-f fa):(optional) Customized database/structures
To use customized databases (e.g. mobile genetic elements or heave metal resistant genes), you need to prepare two files:
database.fasta)structure.txt)The database should be indexed manually (protein or nucleotide, in fasta):
The structure file
structure.txtshould be tab-separated and the first column the sequences ID ofdatabase.fasta(please note that the sequence ID cannot contain space, tab and other irregular char such as forward slash). At lease one column (level 1) is required. For the one column (level 1) case, you may construct the structure file using:One example of the
database.fastaandstructure.txtis :To run args_oap with customized database:
(optional) Stage two pipeline on Galaxy system and download results
(The online version currently does not support SARG v3.0, please use the local version at this moment.)
Go to http://smile.hku.hk/SARGs and using the module ARG_OAP.
Click Execute and you can find four output files for your information
After a while or so, you will notice that their are four files generated for your information.
File 1 and 2: PcoA figures of your samples and other environment samples generated by ARGs abundance matrix normalization to 16S reads number and cell number
File 3 and 4: Other tabular mother tables which including the profile of ARGs type and sub type information, as long as with other environment samples mother table. File3 results of ARGs abundance normalization against 16S reads number; File 4 results of ARGs abundance normalization against cell number
There are some questions raised by users, please refer to the FAQ for details. To run ARG OAP locally, users should download the source code into local computer system (Unix/Linux). Users can upload the generated files for stage two onto our Galaxy analysis platform (http://smile.hku.hk/SARGs) or use the local version of stage two script.
Notice:
This tools only provide the required scripts for ARGs-OAP 3.0 pipeline
This pipeline is distributed in the hope to achieve the aim of management of antibiotic resistant genes in environment, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.This pipeline is only allowed to be used for non-commercial and academic purpose.
The SARG database is distributed only freely used for academic purpose, any commercial use should require the agreement from the developer team.