Myloasm

https://myloasm-docs.github.io/
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Myloasm is a de novo metagenome assembler for long-read sequencing data that produces polished,...
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### Install via Git and Pip

Source: https://myloasm-docs.github.io/mylotools

Clone the repository and install the package locally using pip.

```bash
git clone https://github.com/bluenote-1577/mylotools
cd mylotools

## assuming you have python3 installed
pip install .
```

--------------------------------

### Build from source on x86-64

Source: https://myloasm-docs.github.io/install

Clones the repository and installs the latest development version using cargo.

```bash
git clone https://github.com/bluenote-1577/myloasm --recurse-submodules  
cd myloasm
cargo install --path . 
myloasm -h
```

--------------------------------

### Run myloasm Assembly

Source: https://myloasm-docs.github.io/cmd

Examples for running assembly on Nanopore and PacBio HiFi datasets.

```bash
myloasm nanopore_reads.fq.gz -o output_directory -t 50
```

```bash
myloasm pacbio_reads.fq.gz -o output_directory -t 50 --hifi
```

--------------------------------

### Install via Conda

Source: https://myloasm-docs.github.io/mylotools

Install the package using the bioconda channel.

```bash
mamba install -c bioconda mylotools
```

--------------------------------

### Contig FASTA Record Label Example

Source: https://myloasm-docs.github.io/output

Example of a FASTA header line for a contig generated by myloasm.

```text
>u2658272ctg_len-2275750_circular-possibly_depth-10-9-9_duplicated-no mult=1.00
```

--------------------------------

### Install via Bioconda

Source: https://myloasm-docs.github.io/install

Installs both myloasm and mylotools on x86-64 systems with AVX2 support.

```bash
mamba install -c bioconda myloasm mylotools
```

--------------------------------

### Visualize myloasm output

Source: https://myloasm-docs.github.io/usage

Install and run mylotools to generate quality control reports and visualizations from the assembly output directory.

```bash
# if you haven't installed mylotools
conda install -c bioconda mylotools

cd output_directory
mylotools report --output report_and_plots
ls report_and_plots/contig_summary_report.html
```

--------------------------------

### Contig Information Format

Source: https://myloasm-docs.github.io/output

Example of a segment line in the GFA file representing contig metadata.

```text
S       u165592ctg              LN:i:1034269    DP:f:25.0       DP2:f:24.0      DP3:f:23.0      MEDIAN_DP1:f:35.0
```

--------------------------------

### Read Information Format

Source: https://myloasm-docs.github.io/output

Example of read alignment lines within the GFA file, detailing read contributions and overlap metrics.

```text
a       u165592ctg,0-28710      165592  0       SRRX.2+split0       -       28710   DP1:22,DP2:22,DP3:21,READ_LEN:43601,OL_LEN_NEXT:14808,SNP_SHARE_NEXT:216,SNP_DIFF_NEXT:1
a       u165592ctg,34-6529      1421634 28710   SRRX.1+split0+split0        +       6495    DP1:42,DP2:42,DP3:13,READ_LEN:21212,OL_LEN_NEXT:14629,SNP_SHARE_NEXT:129,SNP_DIFF_NEXT:0
```

--------------------------------

### Navigate to Assembly Output

Source: https://myloasm-docs.github.io/mylotools

Prepare the environment by moving into the directory containing the assembly results.

```bash
myloasm reads.fq .... -o myloasm_results
cd myloasm_results
```

--------------------------------

### Download and run portable binary

Source: https://myloasm-docs.github.io/install

Downloads the v0.5.1 binary for x86-64 systems with AVX2, sets execution permissions, and runs it.

```bash
wget https://github.com/bluenote-1577/myloasm/releases/download/v0.5.1/myloasm-0.5.1-x86_64-avx2
chmod +x myloasm-0.5.1-x86_64-avx2
./myloasm-0.5.1-x86_64-avx2
```

--------------------------------

### Display Mylotools Help

Source: https://myloasm-docs.github.io/mylotools

View the available commands and positional arguments for the mylotools CLI.

```bash
usage: mylotools [-h] [--version] {report,sanitize-headers,plot,strain-viz,extract-contigs} ...

positional arguments:
  {report,sanitize-headers,plot,strain-viz,extract-contigs}
    report              Generate comprehensive report with plots for all long contigs
    sanitize-headers    Sanitize FASTA headers by replacing underscores with spaces (creates backup)
    plot                Generate a plot of various statistics for one of myloasm's output contigs (`report` does `plot` for all contigs)
    strain-viz          Visualize overlaps between and within two or more similar contigs
    extract-contigs     Extract contigs > X bp into a folder as its own fasta
    annotate-gfa        Annotate final_contig_graph.gfa with sequence bases from the final assembly
```

--------------------------------

### Build from source for SSE2

Source: https://myloasm-docs.github.io/install

Compiles for systems with SSE2 but lacking AVX2 instructions.

```bash
cargo install --path . --features=sse --no-default-features
```

--------------------------------

### Generate HTML QC Report

Source: https://myloasm-docs.github.io/mylotools

Create a comprehensive HTML report and verify the output file existence.

```bash
mylotools report -o mylo-report
ls mylo-report/contig_summary_report.html
```

--------------------------------

### Build from source for ARM NEON

Source: https://myloasm-docs.github.io/install

Compiles for ARM architectures using NEON instructions.

```bash
cargo install --path . --features=neon --no-default-features
```

--------------------------------

### Assemble PacBio HiFi reads

Source: https://myloasm-docs.github.io/usage

Include the --hifi flag when processing PacBio HiFi data.

```bash
myloasm reads1.fq reads2.fq reads3.fq -o output_directory -t 50 --hifi
```

--------------------------------

### Generate interactive QC report

Source: https://myloasm-docs.github.io/qc_manual

Generates an interactive HTML report for all contigs larger than 300 kbp.

```bash
cd myloasm_output
mylotools report --output html_report
```

--------------------------------

### Assemble Nanopore R10.4 reads

Source: https://myloasm-docs.github.io/usage

Run assembly on multiple FASTQ files with specified output directory and thread count.

```bash
myloasm reads1.fq reads2.fq reads3.fq -o output_directory -t 50
```

--------------------------------

### Resume an incomplete myloasm run

Source: https://myloasm-docs.github.io/FAQ

Use the exist keyword to resume a run from existing checkpoint files in the results directory.

```bash
myloasm exist -o results_directory (options)
```

--------------------------------

### View myloasm directory structure

Source: https://myloasm-docs.github.io/secondary

Visual representation of the file hierarchy generated by the myloasm assembly process.

```text
├── myloasm_(DATE + TIME).log
├── assembly_graphs/
│   ├── unitig_graph-0.gfa
│   ├── after_light_cleaning-1.gfa
│   ├── after_walk_heavy_cleaned-2.gfa
│   └── small_and_tip_bubble-3.gfa
├── 0-cleaning_and_unitigs/
│   └── Read cleaning + mapping files
├── 1-light_resolve/
│   └── Initial graph cleaning files
├── 2-heavy_path_resolve/
│   └── Heavy graph cleaning files
├── 3-mapping/
│   ├── map_to_unitigs.paf.gz
│   └── low_quality_regions.bed
├── binary_temp/
│   └── Large binary files 
└── alternate_assemblies/
    ├── duplicated_contigs.fa
    └── assembly_alternate.fa
```

--------------------------------

### Filter and Analyze Contigs with CheckM2

Source: https://myloasm-docs.github.io/qc

Extract contigs of a specific length and run CheckM2 to identify potential chimeric sequences.

```bash
cd myloasm_results
mylotools extract-contigs --output-folder contigs_dir --min-contig-length X
checkm2 predict --input contigs_dir -x fa -o checkm2_results --threads 40
```

--------------------------------

### Plot single contig analysis

Source: https://myloasm-docs.github.io/qc_manual

Generates a specific plot for a single contig and verifies the output file existence.

```bash
cd myloasm_output
mylotools plot u2912759ctg
ls u2912759ctg_analysis.html
```
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