hisat2-read-statistics-py

name	hisat2-read-statistics-py
description	Use when you need to compute basic read statistics (count, min/max/average length) from FASTQ/FASTA files before or after HISAT2 alignment workflows.
disable-model-invocation	true
user-invocable	true

hisat2-read-statistics-py

Quick Start

• Command: hisat2_read_statistics.py [read_file] [-n READ_COUNT]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_read_statistics.py
• Full reference: See references/help.md

When To Use This Tool

• Use hisat2_read_statistics.py when you want a quick length/profile sanity check on input reads before alignment or simulation.
• It is appropriate for FASTA/FASTQ read files when you need rough counts and min/max/average read lengths without launching a full QC suite.
• Use it to verify read-length assumptions before choosing HISAT2 scoring or simulation parameters.
• It is also useful after synthetic-read generation to confirm outputs roughly match expected read lengths.

Common Patterns

# Sample the default first 10,000 reads
hisat2_read_statistics.py reads.fq.gz

# Increase the sample size
hisat2_read_statistics.py reads.fq.gz -n 100000

# Scan the entire file
hisat2_read_statistics.py reads.fq.gz -n 0

# Check simulated reads before alignment
hisat2_read_statistics.py sim_1.fa

Recommended Workflow

1. Verify the read file format (FASTQ or FASTA) is compatible with HISAT2 tools.
2. Run hisat2_read_statistics.py <read_file> to compute statistics on the first 10,000 reads (default).
3. Use -n flag to adjust sample size (e.g., -n 100000 for larger samples or -n 0 for entire file if supported).
4. Review output to confirm read lengths and counts are within expected ranges before proceeding to alignment.

Guardrails

• The tool samples a subset of reads by default (10,000); statistics may not reflect entire file if -n is not adjusted.
• No --version flag is available; verify installation via --help or the executable path.
• Ensure the input file exists and is readable; the tool expects a valid reads file as the positional argument.
• -n 0 means no sampling cutoff, so the script scans the entire file rather than zero reads