Data Acquisition & Simulation

download_genome_by_accession(
;
    accession,
    outdir,
    compressed
)

Downloads a genomic sequence from NCBI's nucleotide database by its accession number.

Arguments

• accession::String: NCBI nucleotide accession number (e.g. "NC_045512")
• outdir::String: Output directory path. Defaults to current directory
• compressed::Bool: If true, compresses output file with gzip. Defaults to true

Returns

• String: Path to the downloaded file (.fna or .fna.gz)

ncbi_genome_download_accession(
;
    accession,
    outdir,
    outpath,
    include_string
)

Download an accession using NCBI datasets command line tool

the .zip download output to outpath will be unzipped

returns the outfolder

ncbi's default include string is include_string = "gff3,rna,cds,protein,genome,seq-report"

Downloads and extracts a genome from NCBI using the datasets command line tool.

Arguments

• accession: NCBI accession number for the genome
• outdir: Directory where files will be downloaded (defaults to current directory)
• outpath: Full path for the temporary zip file (defaults to outdir/accession.zip)
• include_string: Data types to download (defaults to all "gff3,rna,cds,protein,genome,seq-report").

Returns

• Path to the extracted genome data directory

Notes

• Requires the ncbi-datasets-cli conda package (automatically installed if missing)
• Downloaded zip file is automatically removed after extraction
• If output folder already exists, download is skipped
• Data is extracted to outdir/accession/ncbi_dataset/data/accession

Downloads sequencing reads from NCBI's Sequence Read Archive (SRA).

Downloads reads using fasterq-dump. The function automatically detects whether the data is single-end or paired-end and returns appropriate file paths. Users should apply quality control based on their knowledge of the data type.

Arguments

• srr_identifier: SRA run identifier (e.g., "SRR1234567")
• outdir: Output directory for downloaded files (default: current directory)

Returns

Named tuple with:

• srr_id: The SRA identifier
• outdir: Output directory path
• files: Vector of downloaded file paths (1 file for single-end, 2 for paired-end)
• is_paired: Boolean indicating if data is paired-end

Example

# Download SRA data
result = Mycelia.download_sra_data("SRR1234567", outdir="./data")

# Apply appropriate QC based on data type
if result.is_paired
    # Paired-end data - use paired-end QC
    Mycelia.trim_galore_paired(forward_reads=result.files[1], reverse_reads=result.files[2])
else
    # Single-end data - use single-end QC
    Mycelia.qc_filter_short_reads_fastp(input=result.files[1])
end

Prefetches multiple SRA runs in parallel.

Downloads SRA run files (.sra) to local storage without converting to FASTQ. Useful for batch downloading before processing with fasterq-dump.

Arguments

• srr_identifiers: Vector of SRA run identifiers
• outdir: Output directory for prefetched files (default: current directory)
• max_parallel: Maximum number of parallel downloads (default: 4)

Returns

Vector of named tuples with prefetch results for each SRA run

Example

runs = ["SRR1234567", "SRR1234568", "SRR1234569"]
results = Mycelia.prefetch_sra_runs(runs, outdir="./sra_data")

Parallel FASTQ dump for multiple SRA files.

Converts multiple SRA files to FASTQ format in parallel. More efficient than sequential processing for large batches.

Arguments

• srr_identifiers: Vector of SRA run identifiers
• outdir: Output directory for FASTQ files (default: current directory)
• max_parallel: Maximum number of parallel conversions (default: 2)

Returns

Vector of named tuples with conversion results

Example

runs = ["SRR1234567", "SRR1234568"]
results = Mycelia.fasterq_dump_parallel(runs, outdir="./fastq_data")

simulate_illumina_paired_reads(
;
    in_fasta,
    coverage,
    read_count,
    outbase,
    read_length,
    mflen,
    sdev,
    seqSys,
    amplicon,
    errfree,
    rndSeed
)

Simulate Illumina short reads from a FASTA file using the ART Illumina simulator.

This function wraps ART (installed via Bioconda) to simulate reads from an input reference FASTA. It supports paired-end (or optionally single-end/mate-pair) simulation, with options to choose either fold coverage (--fcov) or an absolute read count (--rcount), to enable amplicon mode, and to optionally generate a zero-error SAM file.

Arguments

• in_fasta::String: Path to the input FASTA file.
• coverage::Union{Nothing,Number}: Desired fold coverage (used with --fcov); if nothing and read_count is provided then fold coverage is ignored. (Default: 20)
• read_count::Union{Nothing,Number}: Total number of reads (or read pairs) to generate (used with --rcount instead of fold coverage). (Default: nothing)
• outbase::String: Output file prefix (default: "$(in_fasta).art.$(coverage)x.").
• read_length::Int: Length of reads to simulate (default: 150).
• mflen::Int: Mean fragment length for paired-end simulations (default: 500).
• sdev::Int: Standard deviation of fragment lengths (default: 10).
• seqSys::String: Illumina sequencing system ID (e.g. "HS25" for HiSeq 2500) (default: "HS25").
• paired::Bool: Whether to simulate paired-end reads (default: true).
• amplicon::Bool: Enable amplicon sequencing simulation mode (default: false).
• errfree::Bool: Generate an extra SAM file with zero sequencing errors (default: false).
• rndSeed::Union{Nothing,Int}: Optional seed for reproducibility (default: nothing).

Outputs

Generates gzipped FASTQ files in the working directory:

• For paired-end: $(outbase)1.fq.gz (forward) and $(outbase)2.fq.gz (reverse).
• For single-end: $(outbase)1.fq.gz.

Additional SAM files may be produced if --errfree is enabled and/or if the ART --samout option is specified.

Details

This function calls ART with the provided options. Note that if read_count is supplied, the function uses the --rcount option; otherwise, it uses --fcov with the given coverage. Amplicon mode (via --amplicon) restricts the simulation to the amplicon regions, which is important for targeted sequencing studies.

Dependencies

Requires ART simulator (installed via Bioconda) and the Mycelia environment helper.

See also: simulate_nanopore_reads, simulate_nearly_perfect_long_reads, simulate_pacbio_reads

simulate_pacbio_reads(; fasta, quantity, outfile)

Simulate PacBio HiFi reads using the Badread error model.

Arguments

• fasta::String: Path to input FASTA file containing reference sequence
• quantity::String: Coverage depth (e.g. "50x") or total bases (e.g. "1000000") - NOT TOTAL READS
• outfile::String: Output filepath for simulated reads. Defaults to input filename with ".badread.pacbio2021.{quantity}.fq.gz" suffix

Returns

• String: Path to the generated output file

Notes

• Requires Badread tool from Bioconda
• Uses PacBio 2021 error and quality score models
• Average read length ~15kb
• Output is gzipped FASTQ format

See also: simulate_nanopore_reads, simulate_nearly_perfect_long_reads, simulate_short_reads

simulate_nanopore_reads(; fasta, quantity, outfile)

Simulate Oxford Nanopore sequencing reads using the Badread tool with 2023 error models.

Arguments

• fasta::String: Path to input reference FASTA file
• quantity::String: Either fold coverage (e.g. "50x") or total bases to sequence (e.g. "1000000")
• outfile::String: Output path for gzipped FASTQ file. Defaults to input filename with modified extension

Returns

• String: Path to the generated output FASTQ file

See also: simulate_pacbio_reads, simulate_nearly_perfect_long_reads, simulate_short_reads