| abPOA | | https://github.com/yangao07/abPOA |
| ABRA | v2.23 | https://github.com/mozack/abra |
| Bandage | v0.8.1 | https://rrwick.github.io/Bandage/ |
| bcftools | v1.16 | https://samtools.github.io/bcftools/ |
| BEDTools | v2.28.0, v2.30.0 | https://bedtools.readthedocs.io/en/latest/ |
| Bowtie2 | v2.4.5 | https://github.com/BenLangmead/bowtie2 |
| BWA-MEM | v0.7.17-r1188 | https://github.com/lh3/bwa |
| Cactus | 6cd9a42 | https://github.com/ComparativeGenomicsToolkit/cactus |
| Comparative Annotation Toolkit (CAT) | eb2fc87 | https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit |
| danbing-tk | v1.3 | https://github.com/ChaissonLab/danbing-tk |
| DeepVariant | v1.3.0 | https://github.com/google/deepvariant |
| Dfam | v3.3 | https://www.dfam.org/home |
| Dipcall | v0.3 | https://github.com/lh3/dipcall |
| dna-brnn | v0.1 | https://github.com/lh3/dna-brnn |
| Exact Tandem Repeat Finder (ETRF) | fc059d5 | https://github.com/lh3/etrf |
| Exonerate | | https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate |
| Flagger | v0.1 | https://github.com/mobinasri/flagger |
| FreeBayes | v1.2.0 | https://github.com/freebayes/freebayes |
| GATK | v3.8.1 | https://gatk.broadinstitute.org/hc/en-us |
| gfabase | v0.6.0 | https://github.com/mlin/gfabase |
| GFAffix | v0.1.3 | https://github.com/marschall-lab/GFAffix |
| GFAools | v0.5 | https://github.com/lh3/gfatools |
| GffRead | v0.12.7 | https://github.com/gpertea/gffread |
| gggenes | v0.4.1 | https://github.com/wilkox/gggenes |
| Graph Peak Caller | v1.2.3 | https://github.com/uio-bmi/graph_peak_caller |
| GraphAligner | v1.0.13 | https://github.com/maickrau/GraphAligner |
| hal2vg | | https://github.com/ComparativeGenomicsToolkit/hal2vg |
| Hall-lab pipeline | 830260a | https://github.com/hall-lab/competitive-alignment/blob/master/call_assembly_variants.wdl |
| halLiftover | | https://github.com/ComparativeGenomicsToolkit/hal |
| hap.py | v3.15 | https://github.com/Illumina/hap.py |
| HiFiAdapterFilt | 64d1c7b | https://github.com/sheinasim/HiFiAdapterFilt |
| hifiasm | v0.14, v0.14.1 | https://github.com/chhylp123/hifiasm |
| Illumina's Dragon platform | v3.7.5 | https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/Informatics/DRAGEN/GraphMapper_fDG.htm |
| Integrative Genome Browser (IGV) | | https://software.broadinstitute.org/software/igv/ |
| Iris | v1.0.4 | https://github.com/mkirschle/Iris |
| Liftoff | v1.6.3 | https://github.com/agshumate/Liftoff |
| MAFFT | | https://mafft.cbrc.jp/alignment/software/ |
| Mercury | 261b085 | https://github.com/marbl/mercury |
| meryl | 6d396a0 | https://github.com/marbl/meryl |
| Minigraph | v0.14, v0.18 | https://github.com/lh3/minigraph |
| minimap2 | v2.21, v2.1, v2.2.4 | https://github.com/lh3/minimap2 |
| NCBI/RMBLAST | v2.10.0 | http://www.repeatmasker.org/rmblast/ |
| odgi pangenome analysis toolkit | | https://github.com/pangenome/odgi |
| panacus | 1eeb6d0 | https://github.com/marschall-lab/panacus |
| PanGenie | v1.0.0 | https://github.com/eblerjana/pangenie |
| PanGenome Graph Builder (PGGB) | v0.2.0+531f85f | https://github.com/pangenome/pggb |
| PAV | v0.9.1 | https://github.com/EichlerLab/pav |
| PBSV | v2.6.2 | https://github.com/PacificBiosciences/pbsv |
| Pstools | v0.1 | https://github.com/shilpagarg/pstools |
| QUAST | v5.0.2 | https://quast.sourceforge.net/ |
| RepeatMasker | v4.1.2-p1 | https://www.repeatmasker.org/ |
| RPGV | 1d91a9e | https://github.com/jonassibbesen/rpgv |
| RSEM | v1.3.3 | https://github.com/deweylab/RSEM |
| RTG Tools | v3.12.1 | https://github.com/RealTimeGenomics/rtg-tools |
| Salmon | v1.9.0 | https://github.com/COMBINE-lab/salmon |
| Samtools | v1.3.1, v1.15 | https://github.com/samtools/samtools |
| SDUST | v0.1 | https://github.com/lh3/sdust |
| Secphase | v0.1 | https://github.com/mobinasri/secphase |
| sedef | | https://github.com/vpc-ccg/sedef |
| seqtk | v1.3 | https://github.com/lh3/seqtk |
| seqwish | | https://github.com/ekg/seqwish |
| slivar | v0.2.7 | https://github.com/brentp/slivar |
| smoothxg | | https://github.com/pangenome/smoothxg |
| Sniffles | v1.0.12b | https://github.com/fritzsedlazeck/Sniffles |
| STAR | v2.7.10a | https://github.com/alexdobin/STAR |
| SVIM | v2.0.0 | https://github.com/eldariont/svim |
| SVIM-asm | v1.0.2 | https://github.com/eldariont/svim-asm |
| svtools | | https://github.com/hall-lab/svtools |
| Tandem Repeat Finder (TRF) | v4.09 | https://tandem.bu.edu/trf/trf.desc.html |
| truvari | v3.2.0, v3.1.0 | https://github.com/ACEnglish/truvari |
| vcfbub | v0.1.0 | https://github.com/pangenome/vcfbub |
| vcflib | | https://github.com/vcflib/vcflib |
| vg, vg giraffe | v1.33.0, v1.36.0, v1.37.0, v1.38.0, v1.39.0, v1.43.0, 2cea1e2, c0c4816 | https://github.com/vgteam/vg |
| wfmash | | https://github.com/waveygang/wfmash |
| WhatsHap | v1.1 | https://whatshap.readthedocs.io/en/latest/ |
| winnowmap | v2.03 | https://github.com/marbl/Winnowmap |
| Yak | v0.1 | https://github.com/lh3/yak |