Table 1.
Assembly pipeline and software used.
| Assembly step | Software and non-default options | Version | References |
|---|---|---|---|
| Filtering PacBio HiFi adapters | HiFiAdapterFilt | Commit 64d1c7b | Sim et al. (2022) |
| K-mer counting | Meryl (k = 21) | 1 | https://github.com/marbl/meryl |
| Estimation of genome size and heterozygosity | GenomeScope | 2 | Ranallo-Benavidez et al. (2020) |
| De novo assembly (contiging) | HiFiasm (HiC Mode, –primary, output hic.p_ctg, hic.a_ctg) | 0.16.1-r375 | Cheng et al. (2022) |
| Scaffolding | |||
| Omni-C data alignment | Arima Genomics Mapping Pipeline | Commit 2e74ea4 | https://github.com/ArimaGenomics/mapping_pipeline |
| Arima Genomics Mapping Pipeline (AGMP) | BWA-MEM | 0.7.17-r1188 | Li (2013) |
| samtools | 1.11 | Danecek et al. (2021) | |
| filter_five_end.pl (AGMP) | Commit 2e74ea4 | https://github.com/ArimaGenomics/mapping_pipeline | |
| two_read_bam_combiner.pl ((AGMP)) | Commit 2e74ea4 | https://github.com/ArimaGenomics/mapping_pipeline | |
| picard | 2.27.5 | https://broadinstitute.github.io/picard/ | |
| Omni-C Scaffolding | SALSA (-DNASE, -i 20, -p yes) | 2 | Ghurye et al. (2017, 2019) |
| Omni-C Contact map generation | |||
| Short-read alignment | BWA-MEM (-5SP) | 0.7.17-r1188 | Li (2013) |
| SAM/BAM processing | samtools | 1.11 | Danecek et al. (2021) |
| SAM/BAM filtering | pairtools | 0.3.0 | Open2C et al. (2023) |
| Pairs indexing | pairix | 0.3.7 | Lee at al. (2022) |
| Matrix generation | cooler | 0.8.10 | Abdennur and Mirny (2020) |
| Matrix balancing | hicExplorer (hicCorrectmatrix correct --filterThreshold -2 4) | 3.6 | Ramírez et al. (2018) |
| Contact map visualization | HiGlass | 2.1.11 | Kerpedjiev et al. (2018) |
| PretextMap | 0.1.4 | https://github.com/wtsi-hpag/PretextView | |
| PretextView | 0.1.5 | https://github.com/wtsi-hpag/PretextMap | |
| PretextSnapshot | 0.0.3 | https://github.com/wtsi-hpag/PretextSnapshot | |
| Manual curation tools | Rapid curation pipeline (Wellcome Trust Sanger Institute, Genome Reference Informatics Team) | Commit 7acf220c | https://gitlab.com/wtsi-grit/rapid-curation |
| Genome quality assessment | |||
| Basic assembly metrics | QUAST (--est-ref-size) | 5.0.2 | Gurevich et al. (2013) |
| Assembly completeness | BUSCO (-m geno, -l mammalia) | 5.0.0 | Manni et al. (2021) |
| Merqury | 2020-01-29 | Rhie et al. (2020) | |
| Contamination screening | |||
| Local alignment tool | BLAST + (-db nt, -outfmt “6 qseqid staxids bitscore std,” -max_target_seqs 1, -max_hsps 1, -evalue 1e-25) | 2.10 | Camacho et al. (2009) |
| General contamination screening | BlobToolKit (PacBIo HiFi Coverage, NCBI Taxa ID = 9643, BUSCODB = mammalia) | 2.3.3 | Challis et al. (2020) |
| Mitochondrial assembly | |||
| Mitochondrial genome assembly | MitoHiFi (-r, -p 90, -o 1) | 2.2 | Uliano-Silva et al. (2023) |
| Synteny analysis | |||
| Sequence alignment tool | mummer (nucmer) | 3.1 | Kurtz et al. (2004) |