⚠️⚠️⚠️ symcla is being archived and its development will continue as part of the symclatron project ⚠️⚠️⚠️

symcla: symbiont classifier

💾 Installation

Clone the symcla repository:

{shell} git clone https://github.com/NeLLi-team/symcla.git

{bash} cd symcla/ chmod u+x symcla

Create conda environment and install requirements:

{bash} conda create -c conda-forge -c bioconda --name symcla --file requirements.txt

💽 Setup data (run only once)

Run inside the symcla/ folder:

{shell} conda activate symcla

{shell} ./symcla setup

🚀 Example run

{shell} conda activate symcla

👷🏻‍♀️ Run the classifier

{shell} path_to_symcla/symcla classify --genomedir data/test_genomes --savedir test_output --ncpus 32

To get help

```{bash} ./symcla classify --help

Usage: symcla classify [OPTIONS]

╭─ Options ──────────────────────────────────────────────────────────────────────╮

│ --genomedir TEXT [default: input_genomes] │

│ --savedir TEXT [default: output_symcla] │

│ --ncpus INTEGER [default: 16] │

│ --deltmp --no-deltmp [default: deltmp] │

│ --help Show this message and exit. │

╰────────────────────────────────────────────────────────────────────────────────╯

```

🕺🏻 Results

Expected results from the test data:

| taxonoid | completenessUNI56 | featuresgt0| featuresge20 | featuresge100 | symclascore | |-----------------------------------------|--------------------|-------------|---------------|----------------|--------------| | IMGI2140918011 | 98.214 | 396 | 291 | 128 | 0.000 | | IMGI2645727657 | 100.000 | 287 | 197 | 70 | -0.003 | | IMGI651324087 | 100.000 | 368 | 252 | 106 | -0.009 | | IMGM3300027739BIN74 | 64.286 | 310 | 234 | 95 | 0.001 | | SCISO2808607008 | 98.214 | 406 | 276 | 124 | 2.000 | | SDISOGCA003484685.1 | 83.929 | 193 | 126 | 43 | 2.000 | | SHISO2654587767 | 98.214 | 423 | 309 | 134 | 2.000 | | SLISOGCF900639865.1 | 100.000 | 569 | 429 | 234 | 0.999 | | SRISO640427127 | 92.857 | 296 | 197 | 103 | 2.000 | | SXGCA000019745.1 | 98.214 | 353 | 259 | 106 | 0.126 | | SXGCA902860225.1Azoamicus_ciliaticola | 91.071 | 117 | 83 | 36 | 1.055 | | SXISO642555114 | 96.429 | 333 | 243 | 108 | 1.995 |

🧐 Interpretation of results:

• completeness_UNI56: The percentage of 56 universal bacterial and archaeal marker genes found in the genome. We do not advise to trust any results <50%. Confidence in symbiont prediction increases with UNI56 completeness.
• features_gt01: Number of features found with a bitscore greater than 0. Confidence in symbiont prediction increases with more features found.
• features_ge20: Number of features found with a bitscore greater or equal than 20. Confidence in symbiont prediction increases with more features found.
• features_ge100: Number of features found with a bitscore greater or equal than 100. Confidence in symbiont prediction increases with more features found.
• symcla_score: after adjusting the classification thresholds based on thousands of experiments, we recommend the following values:
  • symcla_score <= 0.42: Free-living
  • 0.42 < symcla_score < 1.21: Symbiont;Host-associated
  • symcla_score >= 1.21: Symbiont;Intracellular

🤖 Note: by design symcla minimizes the rate of false positives for symbionts, at the expense of increased false negatives (i.e. some Symbiont;Host-associated might still get a symcla score lower than 0.42, and some Symbiont;Intracellular might still get a symcla score lower than 1.21).

🐳 symcla container

Apptainer

```bash apptainer pull \ docker://docker.io/jvillada/symcla:latest

apptainer run \ docker://docker.io/jvillada/symcla:latest \ symcla \ classify \ --genomedir pathtodirwithfaafiles \ --savedir pathtooutputdir \ --ncpus 16 ```