The datasets can be downloaded from https://zenodo.org/record/6938771#.YuZef3ZByUk !

We evaluate AIM using two types of datasets: (1) real datasets for short sequence pairs, (2) synthetic datasets for long sequence pairs

Real datasets for short sequence pairs (100bp, 150bp, and 250bp long)

The short read-reference pair sets are generated using minimap2 by mapping the following datasets to the human reference genome GRCh37:

1. https://www.ebi.ac.uk/ena/browser/view/ERR240727
2. https://www.ebi.ac.uk/ena/browser/view/SRR826460
3. https://www.ebi.ac.uk/ena/browser/view/SRR826471

The human reference genome can be downloaded from:

ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz

After extracting the read-reference pairs we format the datasets as shown in the samples above.

Synthetic datasets for long sequence pairs (500bp, 1000bp, 5Kbp, and 10Kbp long)

We use the data generator found in WFA's repository (https://github.com/smarco/WFA) to simulate long sequence pairs:

git clone https://github.com/smarco/WFA
cd WFA
make
# Example of generating synthetic dataset with sequence length 100, % edit distance 1% and 5M pairs
./bin/generate_dataset --n 5000000 --l 100 --e 0.01 --o ./synthetic-l100-e1-5MPairs