Almost all of the links will send you to the corresponding repository. The rest of the links correspond to the main documentation web site of the tool.
| Purpose | Program | Version |
|---|---|---|
| Filtering PacBio HiFi adapters | HiFiAdapterFilt | Commit 64d1c7b |
| K-mer counting | meryl | 1 |
| Estimation of genome size and heterozygosity | GenomeScope | 2 |
| de novo assembly (contiging) | HiFiasm | 0.13-r308 |
| Long-read, genome-genome alignment | minimap2 | 2.16 |
| Remove low-coverage, duplicated contigs | purge_dups | 1.0.1 |
| HiC mapping for SALSA | Arima Genomics mapping pipeline | Commit 2e74ea4 |
| HiC Scaffolding | SALSA | 2 |
| Gap closing | YAGCloser | Commit 20e2769 |
| Purpose | Program | Version |
|---|---|---|
| Short-read alignment | bwa | 0.7.17-r1188 |
| SAM/BAM processing | samtools | 1.11 |
| SAM/BAM filtering | pairtools | 0.3.0 |
| Pairs indexing | pairix | 0.3.7 |
| Matrix generation | cooler | 0.8.10 |
| Matrix balancing | hicExplorer | 3.6 |
| Contact map visualization | HiGlass | 2.1.11 |
| Contact map generation | PretextMap | 0.1.4 |
| Contact map visualization | PretextView | 0.1.5 |
| Contact map visualization | PretextSnapshot | 0.0.3 |
| Purpose | Program | Version |
|---|---|---|
| Sequence similarity search | BLAST+ | 2.10 |
| Long read alignment | pbmm2 | 1.4.0 |
| Variant calling and consensus | bcftools | 1.11-5-g9c15769 |
| Extraction of sequences | seqtk | 1.3-r115-dirty |
| Sequence polishing | raptor | 0.20.3-171e0f1 |
| Circular-aware long-read alignment | racon | 1.4.19 |
| Sequence alignment | lastz | 1.04.08 |
| Gene annotation | MitoFinder | 1.4 |
| Purpose | Program | Version |
|---|---|---|
| Basic assembly metrics | QUAST | 5.0.2 |
| Assembly completeness | BUSCO | 5.0.0 |
| k-mer based assembly evaluation | Merqury | 1 |
| Contamination screening | BlobToolKit | 2.3.3 |
- Arctostaphylos glauca