Table 3. Software tools used.
| Software tool | Version | Source |
|---|---|---|
| Falcon-unzip | falcon-kit 1.8.0 | ( Chin et al., 2016) |
| purge_dups | 1.0.0 | ( Guan et al., 2020) |
| Bionano Solve | Solve3.4.1_09262019 | https://bionanogenomics.com/downloads/bionano-solve/ |
| SALSA2 | 2.1 | ( Ghurye et al., 2019) |
| scaff10x | 4.2 | https://github.com/wtsi-hpag/Scaff10X |
| arrow | GCpp-1.9.0 | https://github.com/PacificBiosciences/GenomicConsensus |
| longranger align | longranger align (2.2.2) |
https://support.10xgenomics.com/genome-exome/software/
pipelines/latest/advanced/other-pipelines |
| freebayes | v1.3.1-17-gaa2ace8 | ( Garrison & Marth, 2012) |
| bcftools consensus | 1.11-88-g71d744f8 | http://samtools.github.io/bcftools/bcftools.html |
| HiGlass | 1.11.6 | ( Kerpedjiev et al., 2018) |
| PretextView | 0.0.4 | https://github.com/wtsi-hpag/PretextView |
| gEVAL | N/A | ( Chow et al., 2016) |
| BlobToolKit | 1.2 | ( Challis et al., 2020) |