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cultivarium / MicrobeMod

A toolkit for exploring prokaryotic methylation and base modifications in nanopore sequencing
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MicrobeMod

MicrobeMod is a workflow and toolkit for exploring prokaryotic methylation in nanopore sequencing.

Crits-Christoph, Alexander, Shinyoung Clair Kang, Henry H. Lee, and Nili Ostrov. "MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing." bioRxiv (2023): 2023-11.

Overview of the MicrobeMod pipeline

December 2023 update: MicrobeMod v1.0.3 is now compatible with the 4mC all-context model available through Rerio!

July 2024 update: MicrobeMod v1.0.4 is now compatible with the 4mC_5mC all-context models available through Dorado 0.7+!

Data

FASTQ data (in the form of BAMs mapped to each reference) and POD5 data for the genome set from the MicrobeMod preprint can be downloaded with the commands below. Note that the raw2 POD5 data is substantial (213 GB total).

aws s3 cp --recursive s3://cultivarium-sequencing/MICROBEMOD-DATA-NOV2023/mapped_bams/ .
aws s3 cp --recursive s3://cultivarium-sequencing/MICROBEMOD-DATA-NOV2023/reference_genomes/ .
aws s3 cp --recursive s3://cultivarium-sequencing/MICROBEMOD-DATA-NOV2023/pod5/ .

Installing external dependencies

Before installation, make sure the following external dependencies are available in your path.

Dependencies for MicrobeMod annotate_rm

  1. Prodigal, BLAST, and HMMER:

  2. Cath-resolve-hits: https://github.com/UCLOrengoGroup/cath-tools/releases/tag/v0.16.10

All of the above can easily be installed via conda: 

conda install -c bioconda prodigal hmmer blast cath-tools

Dependencies for MicrobeMod call_methylation

  1. Modkit v0.2.2: https://github.com/nanoporetech/modkit You can also install Modkit via conda: conda install -c nanoporetech modkit.

July 2024 update: MicrobeMod is also compatible with Modkit 0.3 according to our testing.

  1. STREME: https://meme-suite.org/meme/doc/download.html You can also install STREME via conda: conda install -c bioconda meme.

Both can also be installed via conda, although you may run into errors on some systems: 

conda install -c bioconda meme
conda install -c nanoporetech modkit

MicrobeMod installation

git clone https://github.com/cultivarium/MicrobeMod.git
cd MicrobeMod/MicrobeMod/

Download the database (required for annotate_rm only - includes HMMs from DefenseFinder and PFAM and REBASE proteins):

python download_db.py

Install:

cd ../
pip install .

To run all tests:

pytest

Optional: Docker installation

Optionally, we provide a Docker container which can be built to run MicrobeMod without installing the dependencies on the host system. To build it:

docker build -t microbemod -f Dockerfile .

And to subsequently run it:

docker run -v $PWD:/home/ubuntu/ -w /home/ubuntu/ microbemod -h

The -v option will make the local directory available to the docker instance, and files within this directory can be passed to the container and accessed via their local paths.

Quick start

If you have a reference mapped, indexed, and sorted BAM output from Dorado, to run MicrobeMod call_methylation with 10 threads:

MicrobeMod call_methylation -b mapped_reads.bam -r genome_reference.fna -t 10

To run MicrobeMod annotate_rm with 10 threads:

MicrobeMod annotate_rm -f genome_reference.fasta -o genome_reference -t 10

Example BAM and FASTA files are available as:

./tests/test_data/test.bam and ./tests/test_data/EcoliCVM05_GCF_000005845.2_ASM584v2_genomic.fna.

Data

FASTQ data (in the form of BAMs mapped to each reference) and POD5 data for the genome set from the MicrobeMod preprint can be downloaded with the commands below. Note that the raw2 POD5 data is substantial (213 GB total).

aws s3 cp --recursive s3://cultivarium-sequencing/MICROBEMOD-DATA-NOV2023/mapped_bams/ .
aws s3 cp --recursive s3://cultivarium-sequencing/MICROBEMOD-DATA-NOV2023/reference_genomes/ .
aws s3 cp --recursive s3://cultivarium-sequencing/MICROBEMOD-DATA-NOV2023/pod5/ .

Step-by-step tutorial

Step 1: Basecalling with Dorado

The first step for methylation motif identification is running Dorado basecalling with modified basecalling models.

You can download models directly through dorado like so:

dorado download --model dna_r10.4.1_e8.2_400bps_sup@v5.0.0
dorado download --model dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1
dorado download --model  dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1

This downloads the latest (as of July 2024) super high accuracy basecalling model (v5.0.0) and the latest all context 6mA, 5mC, and 4mC modified basecalling models.

You can pass any set of 4mC, 5mC, 6mA, and 5hmC basecalling models to Dorado for MicrobeMod.

The command to run the basecalling should look like the below- the primary input is your directory of pod5 files, here named POD5_LIBRARY_NAME (if you have fast5, you can convert them using pod5 convert fast5: https://pod5-file-format.readthedocs.io/en/latest/docs/tools.html).

This command uses a R10.4.1 basecalling model, and passes two modified basecalling models as well, one for all context 4mC and 5mC and one for all context 6mA.

 dorado basecaller dna_r10.4.1_e8.2_400bps_sup@v5.0.0 [LIBRARY NAME] --modified-bases-models dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1,dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1  > [LIBRARY NAME].bam

The output is an unmapped BAM file with modified base information for each read.

Step 2: Mapping reads to the reference with minimap2

The next step is to map your basecalled reads, including their methylation metadata, to your reference genome. This can be done with samtools and minimap2:

samtools fastq LIBRARY_NAME.bam -T MM,ML | minimap2 -t 14 --secondary=no -ax map-ont -y reference_genomes.fna -| \
samtools view -b | samtools sort -@ 10 -o LIBRARY_NAME.mapped.bam```

The settings for samtools fastq are crucial: -T MM,ML includings the methylation tags in your fastq to pipe to minimap2. Please note that you'll want samtools version v1.11 or later for this step in order to properly transfer the methylation tags.

The settings for minimap2 here are crucial: this turns off secondary alignments (a strange minimap2 default behavior).

The final two samtools lines generate a sorted bam.

You'll then need to index this BAM file:

samtools index LIBRARY_NAME.mapped.bam

Step 3: Run MicrobeMod call_methylation

Now, you are ready to call MicrobeMod call_methylation. This can be done with 10 threads like so:

MicrobeMod call_methylation -b LIBRARY_NAME.mapped.bam -r reference_genomes.fna -t 10

Typically, this command will take 10-20 minutes to successfully run. Upon a completed run, you will see the final lines:

Complete!
Saving methylated site table to: LIBRARY_NAME_methylated_sites.tsv
Saving motif output to: LIBRARY_NAME_motifs.tsv

Parameters to tune

Often, MicrobeMod is robust to the exact parameters used, and the same motifs are returned regardless of these settings. However, there may be tricky motifs or edge cases in which it is valuable to re-run with tweaking these settings:

  1. --min_strand_coverage 10: this is a stranded coverage. So if your genome coverage is 20x, then on average each strand will have 10x coverage. This number should be considerably lower than your actual coverage. If your coverage is as low as 10x, then consider setting this value to --min_strand_coverage 3. I would not recommend much lower than that. You can determine your mean depth of coverage with samtools coverage LIBRARY_NAME.mapped.bam.
  2. --methylation_confidence_threshold 0.66 - this is the confidence threshold that Modkit will use to decide if an individual read is methylated.
  3. --percent_methylation_cutoff 0.66 - this is the percentage of reads mapping to a site that have to be called as methylated to consider that site as methylated. Consider increasing for more stringent motif calling.
  4. --percent_cutoff_streme 0.9 - this is the percentage of reads mapping to a site that have to be called as methylated to pass that site to motif calling. Consider decreasing for broader motif calling.

Tweaking this parameters, and re-running with slightly different ones, may result in more accurate motifs called, and can be worth playing with.

Interpreting Methylation output

The two primary processed output files will be two tab-separated tables, one describing information for all methylated sites (large) and one describing output for methylated motifs (small).

If we look at the motifs results LIBRARY_NAME_motifs.tsv, it might look something like:

Motif Motif_raw Methylation_type Genome_sites Methylated_sites Methylation_coverage Average_Percent_Methylation_per_site Methylated_position_1 Methylated_position_1_percent Methylated_position_2 Methylated_position_2_percent
GATC 1-YGNYGATCNBNHNVN a 38248 38216 0.999 0.93 2 50.0 3 50.0
CCWGG 2-NNSVRCCWGGYBSNN a 24100 14242 0.591 0.83 3 100.0 NA 0
GCACNNNNNNGTT 3-GCACBVNVNNGTTN a 595 595 1.0 0.9 3 48.595 12 48.099
No Motif Assigned NA a NA 9163 NA 0.77 NA NA NA NA
CCWGG 1-NNNNRCCWGGYNNNN m 24100 24086 0.999 0.94 2 48.87 4 48.87
No Motif Assigned NA m NA 542 NA 0.72 NA NA NA NA

Here is a brief description of the columns:

  1. Motif: A consensus motif sequence called.
  2. Motif_raw: The raw motif called by STREME before cleaning up by MicrobeMod. Almost always overly specific.
  3. Methylation_type: currently either a for 6mA or m for 5mC.
  4. Genome_sites: The number of occurrences of this motif in the genome (total).
  5. Methylated_sites: The number of times this motif was actually methylated in the genome.
  6. Methylation_coverage: the rato of the two previous columns.
  7. Average_Percent_Methylation_per_site: The mean of the percent of mapped reads that were methylated at all sites of this motif. Higher = higher confidence methylation calls.
  8. Methylated_position_1: The most frequently methylated position in the motif (1-based indexing). For example, in the first row above, "2" means that A in GATC is methylated.
  9. Methylated_position_1_percent: The percent of motif occurrences at which Methylated_position_1 is methylated. 50% for "A" GATC in GATC (because it is palindromic, and 50% of the time it will be the reverse complement).
  10. Methylated_position_2: The second most frequently methylated position in the motif.
  11. Methylatd_position_2_percent: The percent of motif occurrences at which Methylated_position_2 is methylated.

The LIBRARY_NAME_methylated_sites.tsv is considerable larger, and contains information about every genomic site that was methylated (including their assigned motifs).

Step 4: Run MicrobeMod annotate_rm

The MicrobeMod annotate_rm pipeline is very simple: it just requires any genome assembly, and is not nanopore-specific. You can run it like this:

MicrobeMod annotate_rm -f genome_reference.fasta -o genome_reference -t 10

You can pass either a genome FASTA file with the -f argument, or a genbank file (e.g. downloaded from NCBI) with the -g argument. With -f, prodigal is run to call genes; -g will use gene loci from the GenBank file and skip gene calling.

Interpreting RM gene output

The following files are then created:

test.blast: Raw BLAST results of RM proteins to REBASE
test.faa: Prodigal .faa file (all proteins)
test.hits: Raw output of HMMER
test.resolved.hits: Resolved best HMMER hits 
test.rm.genes.faa: A FASTA file of RM proteins identified in this study
test.rm.genes.tsv: Tabular output describing RM genes

The *.rm.genes.tsv file will look something like this:

Operon Gene System Type Gene type HMM Evalue REBASE homolog Homolog identity(%) Homolog methylation Homolog motif
RM Operon #1 NODE_3_length_585136_cov_9.720044_91 RM_Type_IIG IIG Type_IIG_3 3.7e-182 Bfr4856TORF10500P 100.0 m6A GANGGAG
RM Operon #2 NODE_3_length_585136_cov_9.720044_276 RM_Type_I RE Type_I_REases_FAM_2.einsi_trimmed 7.2e-27 Bfr14ORF3855P 100.0
RM Operon #2 NODE_3_length_585136_cov_9.720044_277 RM_Type_I MT Type_I_MTases_FAM_1 1.1e-164 M.Bsp2737ORF11960P 100.0 m6A
RM Operon #2 NODE_3_length_585136_cov_9.720044_280 RM_Type_I SP Type_I_S_52 8.9e-32 S.Bfr1512ORF18655P 100.0
RM Operon #3 NODE_4_length_554179_cov_10.591782_322 RM_Type_II RE Type_II_REase09 7.1e-17 Bfr4856TORF22075P 100.0 ATGCAT
RM Operon #3 NODE_4_length_554179_cov_10.591782_323 RM_Type_II MT Type_II_MTases_FAM_1 7.3e-89 M.Bfr4856TORF22075P 100.0 ATGCAT
RM Operon #4 NODE_5_length_489011_cov_9.441508_131 RM_Type_IV RE Type_IV_21-RM_Type_IV__Type_IV_REases 3.8e-113
RM Operon #5 NODE_6_length_416426_cov_9.438798_313 RM_Type_I RE Type_I_REases_FAM_0.einsi_trimmed 5.5e-199 Bfr4856TORF13485P 100.0
RM Operon #5 NODE_6_length_416426_cov_9.438798_311 RM_Type_I MT Type_I_MTases_FAM_0 1.5e-172 M.Bfr4856TORF13485P 100.0 m6A
RM Operon #5 NODE_6_length_416426_cov_9.438798_310 RM_Type_I SP Type_I_S_51 9.9e-53 S1.Bfr1512ORF16830P 100.0 GACNNNNNGRTY
RM Operon #5 NODE_6_length_416426_cov_9.438798_307 RM_Type_I SP Type_I_S_01 1.3e-35 S4.Bfr1512ORF16830P 100.0
Singleton #1 NODE_17_length_27965_cov_10.731518_5 RM_Type_II RE Type_II_REase06 4.2e-09
Singleton #2 NODE_1_length_700861_cov_9.167701_172 RM_Type_II MT Type_II_MTases_FAM_33 1e-12
Singleton #3 NODE_3_length_585136_cov_9.720044_324 RM_Type_II MT Type_II_MTases_FAM_5 5.7e-05 M.Hgu7ORFBP 100.0

Each line describes an individual gene: Genes are grouped by whether they are in an "operon" (complete RM system - for Type IV and Type IIG this is just one gene) or are a "singleton" (methyltransferase or RE without a pair).

Description of columns:

  1. Operon: The operon number for a given gene
  2. Gene: The gene name (designated by prodigal).
  3. System Type: The predicted RM system type of that gene.
  4. Gene type: The number of gene (either MT, SP, RE, or IIG)
  5. HMM: The exact HMM that hit that gene.
  6. Evalue: The Evalue of the HMM hit.
  7. REBASE homolog: closest homolog in the REBASE dataset.
  8. Homology identity: Amino acid percent identity of closest hit.
  9. Homolog methylation: The methylation type of the closest homolog, if known.
  10. Homolog motif: The motif specificity of the closest homolog, if known.

MicrobeMod call_methylation: all parameters

usage: MicrobeMod call_methylation [-h] -b BAM_FILE -r REFERENCE_FASTA [-m METHYLATION_TYPES] [-o OUTPUT_PREFIX] [-s STREME_PATH] [--min_strand_coverage MIN_STRAND_COVERAGE]
                                   [--methylation_confidence_threshold METHYLATION_CONFIDENCE_THRESHOLD] [--percent_methylation_cutoff PERCENT_METHYLATION_CUTOFF]
                                   [--percent_cutoff_streme PERCENT_CUTOFF_STREME] [-t THREADS]

optional arguments:
  -h, --help            show this help message and exit
  -b BAM_FILE, --bam_file BAM_FILE
                        BAM file of nanopore reads mapped to reference genome with the MM and ML tags preserved.
  -r REFERENCE_FASTA, --reference_fasta REFERENCE_FASTA
                        Reference genome FASTA file.
  -m METHYLATION_TYPES, --methylation_types METHYLATION_TYPES
                        Methylation types to profile
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Output prefix. Default is based on the BAM filename.
  -s STREME_PATH, --streme_path STREME_PATH
                        Path to streme executable.
  --min_strand_coverage MIN_STRAND_COVERAGE
                        Minimum coverage required to call a site as methylated. Note this is per strand (so half of total coverage). Default: 10x
  --methylation_confidence_threshold METHYLATION_CONFIDENCE_THRESHOLD
                        The minimum confidence score to call a base on a read as methylated. Passed to modkit. Default: 0.66
  --percent_methylation_cutoff PERCENT_METHYLATION_CUTOFF
                        The fraction of methylated reads mapping to a site to count that site as methylated. Default: 0.66
  --percent_cutoff_streme PERCENT_CUTOFF_STREME
                        The fraction of methylated reads mapping to a site to pass that site to motif calling. Default: 0.9
  -t THREADS, --threads THREADS
                        Number of threads to use. Only the first step (modkit) is multithreaded.

MicrobeMod annotate_rm: all parameters

usage: MicrobeMod annotate_rm [-h] [-f FASTA] [-g GENBANK] [-o OUTPUT_PREFIX] [-t THREADS]

optional arguments:
  -h, --help            show this help message and exit
  -f FASTA, --fasta FASTA
                        FASTA file for a genome. This option runs gene calling with prodigal. Either --fasta or --genbank is required.
  -g GENBANK, --genbank GENBANK
                        GenBank (gbk or gbff) file with coding regions annotated as CDS features. No gene calling is run. Either --fasta or --genbank is required.
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
                        Output prefix.
  -t THREADS, --threads THREADS
                        Number of threads to use.

More questions? Open an issue and I will respond!