A snakemake workflow for comprehensive analysis of toxin-antitoxin systems
The mTAS is a pipeline for toxin-antitoxin (TA) analysis. Using a curated reference database, mTAS conducts homology-based strategy to identify TA gene hits and produce reliable, deduplicated homologs. The mTAS accecpts both genome assemblies and high-throughput sequencing data and produce a summary of grouped by TA families.
The curated database consis of references from different sources in cluding TADB2, T1TAdb, TASmania and some sequences curated from previous studies. These reference records covers type I ~ VIII TA classes
- 0.1.4
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fastp >= 0.20
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histat 2.1.0
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Blast+ >= 2.10.1
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(optional) hs-blastn 2.0.0
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(optional) diamond v2.0.6.144
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(optional) prodigal
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viralVerify
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Python 3 (tested in 3.8.3 / 3.6.9 )
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Snakemake >= 7.8.0
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Pandas >= 1.3.4
git clone https://github.com/YuLab-SMU/mTAS.git
Given a folder containin input fasta/fastq files, run the wrapper script run_pipe.sh under the root path.
ind=/PATH/TO/FASTQ
oud=/PATH/FOR/STORING/OUTPUT
bash run_pipe.sh $ind $oud
By default, parameters were stored in the config/params.yaml, these could be adjusted based on your needs. Another way is modifying the smk files stored in the rule direcotry.
The config/config.yaml contains prefined folders for storing intemediate files. You may also modified for your convenience.