best

Bam Error Stats Tool (best): analysis of error types in aligned reads.

best is used to assess the quality of reads after aligning them to a reference assembly.

Features

• Collect overall and per alignment stats
• Distribution of indel lengths
• Yield at different empirical Q-value thresholds
• Bin per read stats to easily examine the distribution of errors for certain types of reads
• Stats for regions specified by intervals (BED file, homopolymer regions, windows etc.)
• Stats for quality scores vs empirical Q-values
• Multithreading for speed

Usage

The best Usage Guide gives an overview of how to use best.

Installing

1. Install Rust.
2. Clone this repository and navigate into the directory of this repository.
3. Run cargo install --locked --path .
4. Run best input.bam reference.fasta prefix/path

This will generate stats files with the prefix/path prefix.

Development

Running

1. Install Rust.
2. Clone this repository and navigate into the directory of this repository.
3. Run cargo build --release
4. Run cargo run --release -- input.bam reference.fasta prefix/path or target/release/best input.bam reference.fasta prefix/path

This will generate stats files with the prefix/path prefix.

The built binary is located at target/release/best.

Formatting

cargo fmt

Comparing

Remember to pass the -t 1 option to ensure that only one thread is used for testing. Best generally tries to ensure the order of outputs is deterministic with multiple threads, but the order of per-alignment stats is arbitrary unless only one thread is used.

Disclaimer

This is not an official Google product.

The code is not intended for use in any clinical settings. It is not intended to be a medical device and is not intended for clinical use of any kind, including but not limited to diagnosis or prognosis.

No representations or warranties are made with regards to the accuracy of results generated. User or licensee is responsible for verifying and validating accuracy when using this tool.