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Metagenomic binning with semi-supervised siamese neural network

Project description

SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks

Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.

Test Status Documentation Status License: MIT

NOTE: This tool is still in development. You are welcome to try it out and feedback is appreciated, but expect some bugs/rapid changes until it stabilizes. Please use Github issues for bug reports and the SemiBin users mailing-list for more open-ended discussions or questions.

Install

SemiBin runs on Python 3.6-3.9.

Install from bioconda

conda create conda create -n SemiBin python==3.7
conda activate SemiBin
conda install -c bioconda semibin

Install from source

You can download the source code from github and install.

Install dependence packages using conda: MMseqs2, Bedtools, Hmmer, Fraggenescan.

conda install -c conda-forge -c bioconda mmseqs2=13.45111
conda install -c bioconda bedtools hmmer fraggenescan==1.30

Once the dependencies are installed, you can install by running:

python setup.py install

Examples

NOTE: The SemiBin API is a work-in-progress. The examples refer to version 0.3, but this may change in the near future (after the release of version 1.0, we expect to freeze the API for at least 5 years. We are very happy to hear any feedback on API design, though.

Easy single/co-assembly binning mode

You will need the following inputs:

  1. A contig file (contig.fna in the example below)
  2. BAM files from mapping short reads to the contigs

The single_easy_bin command can be used in single-sample and co-assembly binning modes (contig annotations using mmseqs with GTDB reference genome) to get results in a single step.

SemiBin single_easy_bin -i contig.fna -b *.bam -o output

In this example, SemiBin will download GTDB to $HOME/.cache/SemiBin/mmseqs2-GTDB/GTDB. You can change this default using the -r argument.

You can set --recluster to use the reclustering step with single-copy genes described in the paper, which can make results a little better.

You can use --environment with (human_gut, dog_gut, or ocean) to use one of our built-in models. (Note: Recommended way, which will save much time for contig annotations and model training, and also get very good results)

SemiBin single_easy_bin -i contig.fna -b *.bam -o output --environment human_gut

Easy multi-samples binning mode

The multi_easy_bin command can be used in multi-samples binning modes (contig annotations using mmseqs with GTDB reference genome).

You will need the following inputs.

  1. A combined contig file

  2. BAM files from mapping

For every contig, format of the name is <sample_name>:<contig_name>, where : is the default separator (it can be changed with the --separator argument). Note: Make sure the sample names are unique and the separator does not introduce confusion when splitting. For example:

>S1:Contig_1
AGATAATAAAGATAATAATA
>S1:Contig_2
CGAATTTATCTCAAGAACAAGAAAA
>S1:Contig_3
AAAAAGAGAAAATTCAGAATTAGCCAATAAAATA
>S2:Contig_1
AATGATATAATACTTAATA
>S2:Contig_2
AAAATATTAAAGAAATAATGAAAGAAA
>S3:Contig_1
ATAAAGACGATAAAATAATAAAAGCCAAATCCGACAAAGAAAGAACGG
>S3:Contig_2
AATATTTTAGAGAAAGACATAAACAATAAGAAAAGTATT
>S3:Contig_3
CAAATACGAATGATTCTTTATTAGATTATCTTAATAAGAATATC

You can get the results with one line of code. You can set --recluster to use the reclustering part with single-copy genes described in the paper.

SemiBin multi_easy_bin -i contig_whole.fna -b *.bam -o output

Output

The output folder will contain

  1. Datasets used for training and clustering.

  2. Saved semi-supervised deep learning model.

  3. Output bins.

  4. Some intermediate files.

For every sample, reconstructed bins are in output_bins directory. Using reclustering, reconstructed bins are in output_recluster_bins directory.

For more details about the output, read the docs.

Advanced workflows

You can run individual steps by yourself, which can enable using compute clusters to make the binning process faster (especially in multi-samples binning mode). For example, single_easy_bin includes the following steps: predict_taxonomy,generate_data_single and bin; while multi_easy_bin includes following step: predict_taxonomy, generate_data_multi and bin.

In advanced mode, you can also use our built-in pre-trained model in single-sample binning mode. Here we provide pre-trained models for human gut, dog gut and marine environment. You can just use these models for single-sample binning and it will save much time for contig annotations and model training.

In our experiments, we found that training for every sample then binning would get the best results, but it has significant computational costs (time and memory). Using our provided trained model is a good option and it can also get very good results and still perform significantly better than Metabat2.

A very easy way to run SemiBin with a built-in model (human_gut/dog_gut/ocean):

SemiBin single_easy_bin -i contig.fna -b *.bam -o output --environment human_gut

Another suggestion is that you can pre-train a model from part of your dataset, which can provide a balance as it is faster than training for each sample while achieving better results than a pre-trained model from another dataset.

(1) Generate data.csv/data_split.csv for every sample

SemiBin generate_data_single -i contig.fna -b *.bam -o output

(2) Generate cannot-link for every sample

SemiBin predict_taxonomy -i contig.fna -o output

(3) Train a pre-trained model across several samples

SemiBin train -i *.fna --data *.csv --data-split *.csv -c cannot*.txt -o output --mode several

(4) Bin with the trained model

SemiBin bin -i contig.fna --model model.h5 --data data.csv -o output

Or our built-in model(human_gut, dog_gut or ocean)

SemiBin bin -i contig.fna --data data.csv -o output --environment human_gut

For more details on usage, including information on how to run individual steps separately, read the docs.

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