California Conservation Genomics Project (CCGP) repository for the genome assembly working group.
Content
Overview
This repository contains scripts used for the reference genome assembly efforts of the CCGP.
CCGP reference genomes are assembled following a protocol adapted from Rhie et al. (2021). Assemblies are comprised of 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 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
- Depending on datasets available or ploidy, we are using single or HiC mode on HiFiasm.
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
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: