noamteyssier / gia_benchmark

a benchmark of gia and bedtools on various functionality

gia_benchmark

a benchmark of gia and other gene interval tools on various functionality.

Information

This was originally done using the following versions:

gia == 0.1.16
bedtools == 2.31.0
bedops == 2.4.41
GenomicRanges == 1.54.1

Running the Benchmark

Get-Fasta

To recreate the get-fasta command you'll need to download the homo-sapiens primary assembly:

You can download it easily with ggetrs

cd data/
ggetrs ref -Dd dna

and generate its indexed fasta (.fai)

samtools faidx Homo_sapiens.GRCh38.dna.primary_assembly.fa
cd ../

Benchmark

The benchmarks are run using just and hyperfine.

You'll need to install each of those:

cargo install just hyperfine

Then you can just run:

just bench

And all the benchmarks should run.

Analysis

The visualization of the data can be viewed using the provided notebooks which recreate the analysis within the manuscript.