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leylabmpi / resmico

Identifying misassemblies via deep learning
MIT License
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bioinformatics deep-learning metagenome-assembly metagenomics

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ResMiCo

overview

Introduction

ResMiCo is a deep learning model capable of detecting metagenome assembly errors. ResMiCo's input is summary data derived from re-aligning reads against the putative genomes. ResMiCo's output is a number betwen 0 and 1 representing the likelihood that a particular genome was misassembled.

The tool is divided into two main parts:

Citation

If using ResMiCo in your work, please cite: ResMiCo: increasing the quality of metagenome-assembled genomes with deep learning

Installation

Using pip (easyest, but works only on specific platforms)

Resmico depends on tensorflow, pandas and numpy, each of which coming with its own host of dependency nightmares. We have created pip wheels for python 3.8, 3.9 and 3.10 for both Mac OS (x86) and relatively recent Linux versions (using glibc >= 2.31). :

pip install resmico

Note: resmico depends on tensorflow, so it won't work on Mac machines with Apple silicon.

If you encounter the following error:

ERROR: Could not find a version that satisfies the requirement ResMiCo (from versions: none)
ERROR: No matching distribution found for ResMiCo

you may need to upgrade your pip version. Try running:

pip install --upgrade pip

If you encounter

ERROR: Ignored the following versions that require a different python version: 1.0.12 Requires-Python >=3.8; 1.0.13 Requires-Python >=3.8; 1.1.0 Requires-Python >=3.8; 1.1.1 Requires-Python >=3.8; 1.2.0 Requires-Python >=3.8; 1.2.1 Requires-Python >=3.8; 1.2.2 Requires-Python >=3.8
ERROR: Could not find a version that satisfies the requirement ResMiCo (from versions: none)
ERROR: No matching distribution found for ResMiCo

you need to create an environment with a Python version >=3.8 using e.g. conda:

conda create -n resmico python=3.8
conda activate resmico

From source using pip

If none of the pip wheels is compatible with your system, you can still install resmico relatively easily by installing the dependencies via conda (or mamba) and using pip to install resmico:

git clone https://github.com/leylabmpi/resmico
conda env create -n resmico -f resmico/environment.yml
conda activate resmico
pip install resmico

WARNING: the resmico bioconda recipe is currently set to an old version of resmico. That old version does not match the current user interface (e.g., lacks resmico bam2feat). So, we do not recommend using the bioconda recipe for installing resmico at this time.

Running the ResMiCo package tests

Install pytest and pytest-console-scripts. For example:

mamba install pytest pytest-console-scripts

Run tests with pytest

pytest -s --hide-run-results --script-launch-mode=subprocess ./resmico/tests/

General usage

ResMiCo-SM snakemake pipeline

Use ResMiCo-SM for creating feature files from real data or simulate new data.

See the ResMiCo-SM README

Note resmico bam2feat can also be used to create feature tables from real data: contig fasta files & associated BAM files (mapped reads)

ResMiCo package

Main interface: resmico -h

Note: Although ResMiCo can be run on a CPU, it is orders of magnitude slower than on a GPU, so we only recommend running on CPUs for testing.

Creating feature tables

See resmico bam2feat -h

Predicting with existing model

See resmico evaluate -h

Filtering out misassembled contigs

See resmico filter -h

Training a new model

See resmico train -h

Example 1: predicting misassemblies with the "default" model

If you already have metagenome reads mapped to your contigs, you can process your own data much like in this example.

The model was trained with data produced via mapping Illumina paired-end reads with Bowtie2.

Working directory

mkdir example1 && cd example1

Get the example dataset

The dataset consists of a few UHGG genomes (MAGs) and associated BAM files. The BAM files were generated by using Bowtie2 to map the associated metagenome paired-end reads (from which the MAGs were assembled) to the MAG contigs.

So, the input consists of fasta files (contigs) and BAM files (mapped reads).

A simple tab-delimited table is used to map the fasta & BAM files.

Map file format:

* A tab-delim table with the columns (any order is allowed): 
  * `Taxon` => name associated with the fasta file of contigs
  * `Fasta` => path to the fasta file of contigs
  * `Sample` => name associated with the BAM file 
  * `BAM` => path to the BAM file of reads mapped to the contigs in `Fasta`

See the map.tsv file for an example.

wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_bam2feat.tar.gz
wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_bam2feat.md5
md5sum --check UHGG-n9_bam2feat.md5
tar -pzxvf UHGG-n9_bam2feat.tar.gz && rm -f UHGG-n9_bam2feat.*

Convert BAM files to feature tables

Create a feature table for each sorted BAM file:

resmico bam2feat --outdir features UHGG-n9_bam2feat/map.tsv

Note: the parameters are the same as used for creating the "default" model from Mineeva et al., 2022, which is critical for getting accurate predictions.

Predict misassemblies

resmico evaluate \
  --min-avg-coverage 0.01 \
  --save-path predictions \
  --save-name default-model \
  --dont-verify-insert-size \
  --feature-files-path features

Note: --min-avg-coverage is set to "0.01" here due to the abnormally low coverage in these small example BAM files. DO NOT use such a low coverage cutoff with real data. In the experiments shown in the paper, it was set to 1.

Note: use --dont-verify-insert-size if you have already checked the insert size distribution range of your data once (inclusion criteria) and want to save some time at this run.

Filter contigs

Filter out contigs predicted to be misassembled

resmico filter \
  --outdir filtered predictions/default-model.csv \
  UHGG-n9_bam2feat/*.fna.gz

Note: change the --score-cutoff parameter to alter the number of contigs filtered.

Example2: Training & using a new model

Working directory

mkdir example2 && cd example2

Get the example dataset

Training data: simulated from 10 genomes in the GTDB

wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/genomes-n10_features.tar.gz
wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/genomes-n10_features.md5
md5sum --check genomes-n10_features.md5
tar -pzxvf genomes-n10_features.tar.gz && rm -f genomes-n10_features.*

Test data: simulated from 9 genomes in the UHGG

wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_features.tar.gz
wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_features.md5
md5sum --check UHGG-n9_features.md5
tar -pzxvf UHGG-n9_features.tar.gz && rm -f UHGG-n9_features.*

Filter out contigs predicted to be misassembled

Filter out contigs with prediction scores below a specific cutoff.

resmico filter \
  --outdir filtered-contigs \
  predictions/default-model.csv \
  UHGG-n9_features/fasta/*fna.gz

You may need to adjust the --score-cutoff in order to filter some contigs

Training on the example train data

Train a new model with the example train dataset.

resmico train --log-progress --n-procs 4 --n-epochs 2 \
  --save-path model-n10 --stats-file='' \
  --save-name genomes-n10 \
  --feature-files-path genomes-n10_features

Predict using the "default" model

Using the "default" resmico model from the Mineeva et al., 2022 manuscript. Prediction on the example test data. This provides a comparison to our newly trained model.

resmico evaluate --n-procs 4 \
  --save-path predictions \
  --save-name default-model \
  --feature-files-path UHGG-n9_features/

Tutorials

See the wiki

Notes

Benchmarking

Model evaluation

Benchmarking resmico evaluate on the CAMI2-gut dataset:

CAMI2-gut metagenome assembly stats:

Training

We highly recommend using multiple GPUs for model training on large datasets, as done in the ResMiCo paper. Training on CPUs with such large datasets is not feasbile.