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_reads(
;
    fasta,
    coverage,
    read_count,
    outbase,
    read_length,
    mflen,
    sdev,
    seqSys,
    amplicon,
    errfree,
    paired,
    rndSeed,
    quiet
)

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 (default: "HS25"). Available ART profiles:
  • "GA1": Genome Analyzer I (max length: 36bp or 44bp)
  • "GA2": Genome Analyzer II (max length: 50bp or 75bp)
  • "HS10": HiSeq 1000 (max length: 100bp)
  • "HS20": HiSeq 2000 (max length: 100bp)
  • "HS25": HiSeq 2500 (max length: 125bp or 150bp)
  • "HSXn": HiSeqX v2.5 PCR free (max length: 150bp)
  • "HSXt": HiSeqX v2.5 TruSeq (max length: 150bp)
  • "MSv1": MiSeq v1 (max length: 250bp)
  • "MSv3": MiSeq v3 (max length: 250bp)
  • "MinS": MiniSeq TruSeq (max length: 50bp)
  • "NS50": NextSeq 500 v2 (max length: 75bp)
• paired::Bool: Whether to simulate paired-end reads (default: true). Some systems like MinS only support single-end.
• 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, quiet)

Simulate PacBio HiFi reads using optimized Badread settings.

Uses PacBio 2021 error and quality score models with identity settings optimized for HiFi reads. Follows the recommended PacBio HiFi simulation parameters from the Badread documentation.

Arguments

• fasta::String: Path to input FASTA file containing reference sequence
• quantity::String: Coverage depth (e.g. "50x") or total bases (e.g. "1000000")
• outfile::String: Output filepath for simulated reads. Defaults to input filename with PacBio HiFi suffix
• quiet::Bool=false: If true, suppress badread output to stdout/stderr

Returns

• String: Path to the generated output file

Notes

• Uses pacbio2021 error and quality score models
• Sets identity to 30,3 for HiFi-appropriate accuracy
• Average read length ~15kb
• Output is gzipped FASTQ format

See also: simulate_nanopore_reads, simulate_nearly_perfect_long_reads, simulate_badread_reads

simulate_nanopore_reads(; fasta, quantity, outfile, quiet)

Simulate Oxford Nanopore R10.4.1 sequencing reads using Badread's default settings.

Badread's default settings correspond to Oxford Nanopore R10.4.1 reads of mediocre quality. Uses nanopore2023 error and quality models with default identity and length distributions.

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_nanopore_r941_reads, simulate_badread_reads