4.82. simulate_illumina_reads¶
Generate synthetic Illumina read sets for testing using wgsim. Takes a space-separated string of colon-separated pairs where each pair consists of a GenBank accession and a coverage value (e.g., ‘KJ660346.2:12.5x NC_004296.1:0.9X’), downloads the sequences, and simulates Illumina reads.
4.82.1. Inputs¶
4.82.1.1. Required inputs¶
simulate_illumina_reads.accession_coverage_string
String — Default: None
Space-separated string of colon-separated pairs where each pair consists of a GenBank accession and a coverage value (e.g., 'KJ660346.2:12.5x NC_004296.1:0.9X').
simulate_illumina_reads.download_fasta_from_accession_string.emailAddress
String — Default: None
???
4.82.1.2. Other common inputs¶
simulate_illumina_reads.out_basename
String — Default: "simulated_reads"
Base name for output files.
4.82.1.3. Advanced inputs¶
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simulate_illumina_reads.simulate_reads.coverage_bed
File? — Default: None
Optional BED file specifying coverage per region. If provided, this overrides coverage_string.
simulate_illumina_reads.simulate_reads.indel_extend_probability
Float? — Default: None
Probability an indel is extended (default: 0.3).
simulate_illumina_reads.simulate_reads.indel_fraction
Float? — Default: None
Fraction of mutations that are indels (default: 0.15).
simulate_illumina_reads.simulate_reads.mutation_rate
Float? — Default: None
Base mutation rate (default: 0.001).
simulate_illumina_reads.simulate_reads.outer_distance
Int? — Default: None
Outer distance between paired reads (default: 500bp).
simulate_illumina_reads.simulate_reads.random_seed
Int? — Default: None
Random seed for reproducibility.
simulate_illumina_reads.simulate_reads.read_length
Int? — Default: None
Length of simulated reads (default: 150bp).
4.82.1.4. Other inputs¶
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simulate_illumina_reads.download_fasta_from_accession_string.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.5.21.0"
???
simulate_illumina_reads.simulate_reads.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.5.21.0"
???
simulate_illumina_reads.simulate_reads.machine_mem_gb
Int — Default: 7
???
4.82.2. Outputs¶
simulate_illumina_reads.read_count
Int
???
simulate_illumina_reads.reference_sequences
File
???
simulate_illumina_reads.simulated_reads_bam
File
???
simulate_illumina_reads.viralngs_version
String
???
Generated using WDL AID (1.0.0)