Datasets used in FORAlign

Datasets source

We use GMGC, HIV, CoVID-19 and MPoX datasets to measure our methods.

Citations:

• GMGC: Coelho, L.P., et al. Towards the biogeography of prokaryotic genes. Nature 601, 252–256 (2022).
• HIV: https://www.hiv.lanl.gov/
• CoVID-19: Shu YL, McCauley J. GISAID: Global initiative on sharing all influenza data - from vision to reality. Eurosurveillance. 2017; 22(13):2-4.
• MPoX: Ma Y, Chen M, Bao Y, et al. MPoxVR: A comprehensive genomic resource for monkeypox virus variant surveillance. The Innovation, 2022, 3(5).

Test cases used in WFA2-test program provided by FORAlign

The generated test data is saved in test_case.tar.xz. This data also saved at Zenodo. The following command provides the way to decompress the file:

mkdir test_case
tar xvf test_case.tar.xz -C ./test_case

For every file in test_case folder, the name of file is the source of test cases (e.g., GMGC_20000__GMGC_10000 means the file is generated by test case GMGC_20000 and GMGC_10000 for pairwise sequence alignment, the first sequence is randomly selected in GMGC_20000 file, the second sequence is randomly selected in GMGC_10000 file), the *.ans file is CIGAR string generated by Benchmark (i.e., gap-affine-swg in WFA2).

Test programs

Test programs has compiled in C++20, and the program is static linked (i.e. no extra dependencies, can be runned in any Linux platforms). The programs has stored in wfa2-test-prog folder.

Test results

All tests are tested in Linux. The results are generated by align_benchmark and multiswg_benchmark programs compiled by wfa2-test folder in FORAlign.

Organized results

The organized results is saved in test-result/json folder. The following table shows the content for these datas:

File Name	Content Info	Used in test
9gpu_*core.json	The test result from 9gpu device use the determined number of cores	all of tests
9gpu_benchmark.json	gap-affine-swg result generated by 128 cores	benchmark for anaylzing datas
hpc_56core_cpucnt_anaysis.json	The test result which the CPU percent tested by top is more than 95% generated by 56 cores	condition_variable and Speedup Ratio for swg
hpc_56core_simpletest.json	The test result which the CPU percent tested by top is more than 95% generated by 56 cores, not tested WFA series	t-blocks
hpc_80core_cpucnt_anaysis.json	The test result which the CPU percent tested by top is more than 95% generated by 80 cores	all of tests except Speedup Ratio for swg
hpc_80core_max_memory.json	The maximum memory in Benchmark methods	Methods selection
singlepc_1_12core.json	The test result generated by 12 cores	all of tests except Speedup Ratio for swg
singlepc_2_16core.json	The test result generated by 16 cores	supplemental data
singlepc_2_24core.json	The test result generated by 24 cores	all of tests except Speedup Ratio for swg
9gpu_256core_Alignment_Argument.json	The test result generate for measuring alignment argument	alignment parameter settings in FORAlign section
bowtie2_res.json	The test result between FORAlign, WFA and Bowtie2	Comparison between FORAlign, WFA and Bowtie2 section

Raw Result in test-result/raw.tar.xz file and compress

The raw test cases is in test-result/raw.tar.xz. The following command provides the way to decompress the file:

tar xvf test-result/raw.tar.xz

Files will in test-result/raw folder.