Table 1. Long-read genome sequence alignment tools.
The tools included in the study are highlighted in this study. Further tools from Long-read-tools.org are available in S1.
| Tool | Year | PMID | DOI | Inclusion | If no, why? |
|---|---|---|---|---|---|
| BLASR | 2012 | 22988817 | 10.1186/1471-2105-13-238 | No | Designed only for SMRT seq |
| BWA-MEM | 2011 | NA | arXiv:1303.3997 | No | Superseded by Minimap2 |
| GraphMap | 2016 | 27079541 | 10.1038/ncomms11307 | No | Superseded by GraphMap2 |
| GraphMap2 | 2019 | NA | 10.1101/720458 | Yes | |
| Kart | 2019 | 31057068 | 10.1142/S0219720019500082 | No | Designed only for SMRT, SBS |
| LAMSA | 2016 | 27667793 | 10.1093/bioinformatics/btw594 | No | Depreciated dependencies resulting in seg fault |
| LAST | 2011 | 21209072 | 10.1101/gr.113985.110 | No | Not parameterized for the nuances of current platforms |
| lordFAST | 2018 | 30561550 | 10.1093/bioinformatics/bty544 | No | Runs resulted in partial completion and a seg fault |
| LRA | 2021 | 34153026 | 10.1371/journal.pcbi.1009078 | Yes | |
| Mashmap2 | 2017 | 30423094 | 10.1093/bioinformatics/bty597 | No | Does not use SAM format needed for variant caller |
| MECAT | 2017 | 28945707 | 10.1038/nmeth.4432 | No | Superseded by Mecat2 |
| MECAT2 | 2017 | 28945707 | 10.1038/nmeth.4432 | No | Designed only for SMRT seq |
| Meta-aligner | 2017 | 28231760 | 10.1186/s12859-017-1518-y | No | Designed only for SMRT seq |
| Minimap2 | 2018 | 29750242 | 10.1093/bioinformatics/bty191 | Yes | |
| NGMLR | 2018 | 29713083 | 10.1038/s41592-018-0001-7 | Yes | |
| rHAT | 2015 | 26568628 | 10.1093/bioinformatics/btv662 | No | Designed only for SMRT seq |
| S-ConLSH | 2021 | 33573603 | 10.1186/s12859-020-03918-3 | No | Designed only for SMRT seq |
| smsMap | 2020 | 32753028 | 10.1186/s12859-020-03698-w | No | Does not use SAM format needed for variant caller |
| Winnowmap | 2020 | 32657365 | 10.1093/bioinformatics/btaa435 | No | Superseded by Winnowmap2 |
| Winnowmap2 | 2022 | 35365778 | 10.1101/2020.11.01.363887 | Yes | |
| YAHA | 2012 | 22829624 | 10.1093/bioinformatics/bts456 | No | Not parameterized for the nuances of current platforms |