### 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 ``` === COMPLETE CONTENT === This response contains all available snippets from this library. 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