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V3.0.md

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Version(V3.0)

Overview

Input

  • PacBio HiFi data
  • OmniC sequencing data

Output

The final output corresponds to a diploid assembly, with the primary/alternate approach. We are generating 2 pseudo-haplotypes (primary and alternate). The primary assembly is more complete and consists of longer phased blocks. The alternate consists of haplotigs (contigs of clones with the same haplotype) in heterozygous regions and is not as complete and more fragmented. As explained by Heng Li (here), given the characteristics of the latter, it cannot be considered on its own, but as a complement of the primary assembly.

The update from previos version relies only on the version of HiFiasm (0.15 to 0.16). See details below.

Software

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.

Assembly

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 0.16.1-r375
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

Omni-C Contact map generation

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

Organelle assembly

Purpose Program Version
Mitgenome assembly MitoHiFi 2 Commit c06ed3e

Genome quality assessment

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

Species generated with this pipeline

  • Lynx rufus

Lin M, Escalona M, Sahasrabudhe R, Nguyen O, Beraut E, Buchalski MR, Wayne RK (2022) A Reference Genome Assembly of the Bobcat, Lynx rufus. Journal of Heredity, 113 (6): 615–623, https://doi.org/10.1093/jhered/esac031

  • Mytilus californianus

Paggeot LX, DeBiasse MB, Escalona M, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, Dawson MN (2022) Reference genome for the California ribbed mussel, Mytilus californianus, an ecosystem engineer. Journal of Heredity, 113 (6): 681–688, https://doi.org/10.1093/jhered/esac041

  • Embiotoca jacksoni

Bernardi G, Toy JA, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB (2022) Reference genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California kelp forest fish that lacks a pelagic larval stage. Journal of Heredity, 113 (6): 657–664, https://doi.org/10.1093/jhered/esac034

  • Semicossyphus pulcher

Bernardi G, DeBiasse MB, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Miller C, Toffelmier E, Shaffer HB (2022) Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems. Journal of Heredity, 113 (6): 649-656, https://doi.org/10.1093/jhered/esac032

  • Cebidichthys violaceus

Wright DB, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB, Bernardi G, German DP. (2023) Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus. Journal of Heredity; 114(1):52-59. https://doi.org/10.1093/jhered/esac054

  • Artemisiospiza belli (Paper in progress)
  • Melospiza melodia (Paper in progress)
  • Passerculus sandwichensis (Paper in progress)