California Conservation Genomics Project (CCGP) repository for the genome assembly working group.

Content

• Overview
• Pipeline overview
• Workflows
• Versioning
• Learn more

Overview

This repository contains scripts used for the CCGP's reference genome assembly efforts.

CCGP reference genomes are assembled following a protocol adapted from Rhie et al. (2021). Assemblies comprise PacBio HiFi long read data, which is scaffolded using proximity ligation/chromatin conformation capture (HiC or OmniC) (Dovetail Genomics). Our minimum target reference genome quality is 6.7.Q40, and in most cases, we expect to reach 7.C.Q50 or better (see Table 1 in Rhie et al. (2021)).

Here is the overview of our current pipeline:

Pipeline Overview

There have been multiple versions since the beginning of the project and this is an overview of how the pipeline has evolved.

Color blocks:

• Yellow: sequencing datatypes
• Dark gray: Fixed processes
• Light gray: Optional processes
• Blue: Iterative step

Workflows

Pre-assembly quality control and data validation

• PacBio HiFi
  • PacBio Adapter filtering
  • K-mer counting with meryl
  • Genome size, heterozygosity, and repeat content estimation
  • Coverage validation (calculation of expected coverage given the sequencing data
• HiC/OmniC
  • Library QC with Dovetail Genomics tools

de novo assembly (contigging)

• Contig assembly with HiFiasm
  • We are using single or HiC mode on HiFiasm depending on the datasets available or ploidy.

Purge haplotigs: haplotypic duplications and contig overlaps

• Alignment of HiFi data with minimap2 and purging with purge_dups

Scaffolding

• Alignments with Arima Genomics Mapping Pipeline
• Scaffolding with SALSA

Checking for misassemblies

• Generation and visualization of contact maps
  • HiGlass
  • Generation of tracks
    • HiFi coverage
    • HiC/OmniC coverage
    • Genome assembly mappability
    • Gap description
  • PretextSuite

Gap closing

• Using YAGCloser - based on gap-spanning of long reads

Mitochondrial assembly

• Mitogenome assembly pipeline or MitoHiFi

Contamination screening

• Organelle filtering from nuclear assemblies
• Contamination screening with Blobtools

Metrics/stats/Others

• Contiguity metrics (contig and scaffold N50)
• BUSCO scores
• per base quality / k-mer completeness
• Frameshift errors
• Gap description
• Genome mappability
• Mapping quality

Versioning

• V1.0
• V2.0
• V3.0
• V4.0
• V5.0

Learn more

• For further information about our project and efforts, please redirect to the CCGP website
• For more information about the project, you can also check this:

Shaffer HB, Toffelmier E, Corbett-Detig RB, Escalona M, Erickson B, Fiedler P, Gold M, Harrigan RJ, Hodges S, Luckau TK, Miller C, Oliveira DR, Shaffer KE, Shapiro B, Sork VL, Wang IJ (2022) Landscape genomics to enable conservation actions: the California Conservation Genomics Project. Journal of Heredity, 113 (6): 577–588, https://doi.org/10.1093/jhered/esac020

References

• Rhie A , McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, et al. (2021). Towards complete and error-free genome assemblies of all vertebrate species.Nature. 592:737–746.