hisat2-simulate-reads-py

name	hisat2-simulate-reads-py
description	Use when simulating RNA-seq or DNA-seq reads from a reference genome and GTF annotation file, optionally incorporating SNP variants and controlling expression profiles.
disable-model-invocation	true
user-invocable	true

hisat2-simulate-reads-py

Quick Start

• Command: hisat2_simulate_reads.py [genome_file] [gtf_file] [snp_file] [base_fname]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_simulate_reads.py
• Full reference: See references/help.md for complete options and usage details

When To Use This Tool

• Use hisat2_simulate_reads.py when you need synthetic HISAT2-style benchmark reads from a genome, annotation, and SNP set.
• It is appropriate for RNA-seq by default, but can also simulate DNA-seq with -d.
• Use it when benchmarking alignment settings, validating graph-aware variant handling, or generating controlled test data with fixed read and fragment lengths.
• Reach for it when you need reproducible simulations with explicit random seeds and optional sanity checks.

Common Patterns

# Default paired-end RNA-seq simulation
hisat2_simulate_reads.py genome.fa annotation.gtf variants.snp sim

# Single-end RNA-seq with shorter reads
hisat2_simulate_reads.py genome.fa annotation.gtf variants.snp sim --single-end -r 75 -n 100000

# DNA-seq simulation with explicit random seed
hisat2_simulate_reads.py genome.fa annotation.gtf variants.snp sim -d --random-seed 42

# Run internal sanity checks and print extra statistics
hisat2_simulate_reads.py genome.fa annotation.gtf variants.snp sim --sanity-check -v

Recommended Workflow

1. Prepare a reference genome FASTA file and corresponding GTF annotation file
2. Optionally prepare a SNP file if variant incorporation is needed
3. Run hisat2_simulate_reads.py with required positional arguments and desired options (e.g., -n for fragment count, -e for expression profile)
4. Validate output using --sanity-check and review statistics with -v if needed

Guardrails

• Requires both genome FASTA and GTF files as positional inputs
• Defaults to paired-end RNA-seq reads; use --single-end and/or -d for alternative modes
• Set --random-seed for reproducible simulations
• The script writes output files based on base_fname, including base_fname.sam and at least base_fname_1.fa (plus base_fname_2.fa for paired-end mode)
• In the current environment, -h prints a non-fatal Python SyntaxWarning before the usage text; treat that as a script warning, not a failed invocation