The assembly QC pipeline is an integrated pipeline that begins with screening for foreign contamination, incorporating steps from previously conducted assembly QC pipelines. The following results can be obtained:
- Basic Statistics: Includes N50 for both scaftigs and contigs
- Telomere Region Annotation: BED files generated using seqtk telo
- Saffire result includes assembly to reference PAF
- Gene Completeness Assessment: Compleasm (miniBUSCO)
- Assembly Quality Score (QV): Merqury
- Projection Plot
- ModDotPlot for acrocentric regions: Available for human assemblies only
Example Config: config/config_asm_qc.yaml
### general
MANIFEST: config/manifest_asm_qc.tab
REF:
CHM13:
PATH: /net/eichler/vol28/eee_shared/assemblies/CHM13/T2T/v2.0/T2T-CHM13v2.fasta
CHROMS: /net/eichler/vol28/eee_shared/assemblies/CHM13/T2T/v2.0/genome.txt
CYTO: /net/eichler/vol28/eee_shared/assemblies/CHM13/T2T/v2.0/anno/cyto.bed ## Optional
GRCh38:
PATH: /net/eichler/vol28/eee_shared/assemblies/hg38/no_alt/hg38.no_alt.fa
CHROMS: /net/eichler/vol28/eee_shared/assemblies/hg38/no_alt/genome.txt
CYTO: /net/eichler/vol28/eee_shared/assemblies/hg38/no_alt/anno/cyto.bed ## Optional
### ModDotPlot
BED: config/moddot_regions.bed
### compleasm
DB_PATH: /net/eichler/vol28/eee_shared/buscodb/
LINEAGE: primates
MODE: busco
### foreign contamination screening
TAXID: 9606
Example Manifest ( tab-delemetered )
SAMPLE H1 H2 UNASSIGNED ILLUMINA FOFN TRIO MO_ID FA_ID
unique_sample_name unique_sample_name/assembly.haplotype1.fasta unique_sample_name/assembly.haplotype2.fasta NA sample_name sample_name_illumina.fofn NO NA NA
Begin with a dry-run
./runlocal 30 -np
If dry-run looks good, proceed with:
./runlocal 30
.
├── assembly_stats
│ └── unique_sample_name
│ └── unique_sample_name.tsv
├── compleasm
│ └── results
│ ├── unique_sample_name_hap1
│ │ ├── {database}
│ │ └── summary.txt
│ └── unique_sample_name_hap2
│ ├── {database}
│ └── summary.txt
├── contamination_screening
│ ├── filtered_fasta
│ │ ├── unique_sample_name_hap1.filtered.fasta
│ │ ├── unique_sample_name_hap2.filtered.fasta
│ ├── raw_fasta
│ │ ├── unique_sample_name_hap1.fasta (link to the input hap1 fasta)
│ │ └── unique_sample_name_hap2.fasta (link to the input hap2 fasta)
│ └── results
│ ├── unique_sample_name_hap1
│ └── unique_sample_name_hap2
├── fcs_cleaned_fasta
│ ├── unique_sample_name_hap1
│ │ ├── unique_sample_name_hap1.fasta
│ │ └── contig_fasta
│ │ └── unique_sample_name_hap1.fasta
│ └── unique_sample_name_hap2
│ ├── unique_sample_name_hap2.fasta
│ └── contig_fasta
│ └── unique_sample_name_hap2.fasta
├── merqury
│ ├── meryl
│ │ ├── sample_name
│ │ │ └── sample_name_all.meryl
│ └── results
│ └── unique_sample_name
│ ├── unique_sample_name.unique_sample_name_hap1.qv
│ ├── unique_sample_name.unique_sample_name_hap2.qv
│ ├── unique_sample_name.completeness.stats
│ ├── unique_sample_name.qv
│ ├── unique_sample_name_hap1.meryl
│ └── unique_sample_name_hap2.meryl
├── moddotplot (only for human ; TAXID 9606)
│ ├── contigs
│ │ ├── unique_sample_name_hap1
│ │ └── unique_sample_name_hap2
│ ├── fasta
│ │ ├── unique_sample_name_hap1
│ │ └── unique_sample_name_hap2
│ ├── liftover
│ │ └── paf
│ │ ├── unique_sample_name_hap1
│ │ └── unique_sample_name_hap2
│ ├── results
│ │ ├── unique_sample_name_hap1.generated_acros.tsv
│ │ ├── unique_sample_name_hap2.generated_acros.tsv
│ │ ├── unique_sample_name_hap1 (some can be missing)
│ │ │ ├── CHROM_1_22508596_FULL.pdf
│ │ │ ├── chr13_1_22508596_FULL.png
│ │ │ ├── chr13_1_22508596_TRI.pdf
│ │ │ ├── chr13_1_22508596_TRI.png
│ │ │ ├── chr14_1_17708411_FULL.pdf
│ │ │ ├── chr14_1_17708411_FULL.png
│ │ │ ├── chr14_1_17708411_TRI.pdf
│ │ │ ├── chr14_1_17708411_TRI.png
│ │ │ ├── chr15_1_22694466_FULL.pdf
│ │ │ ├── chr15_1_22694466_FULL.png
│ │ │ ├── chr15_1_22694466_TRI.pdf
│ │ │ ├── chr15_1_22694466_TRI.png
│ │ │ ├── chr21_1_16306378_FULL.pdf
│ │ │ ├── chr21_1_16306378_FULL.png
│ │ │ ├── chr21_1_16306378_TRI.pdf
│ │ │ ├── chr21_1_16306378_TRI.png
│ │ │ ├── chr22_1_20711065_FULL.pdf
│ │ │ ├── chr22_1_20711065_FULL.png
│ │ │ ├── chr22_1_20711065_TRI.pdf
│ │ │ └── chr22_1_20711065_TRI.png
│ │ └── unique_sample_name_hap2 (some can be missing)
│ │ ├── chr13_1_22508596_FULL.pdf
│ │ ├── chr13_1_22508596_FULL.png
│ │ ├── chr13_1_22508596_TRI.pdf
│ │ ├── chr13_1_22508596_TRI.png
│ │ ├── chr14_1_17708411_FULL.pdf
│ │ ├── chr14_1_17708411_FULL.png
│ │ ├── chr14_1_17708411_TRI.pdf
│ │ ├── chr14_1_17708411_TRI.png
│ │ ├── chr15_1_22694466_FULL.pdf
│ │ ├── chr15_1_22694466_FULL.png
│ │ ├── chr15_1_22694466_TRI.pdf
│ │ ├── chr15_1_22694466_TRI.png
│ │ ├── chr21_1_16306378_FULL.pdf
│ │ ├── chr21_1_16306378_FULL.png
│ │ ├── chr21_1_16306378_TRI.pdf
│ │ ├── chr21_1_16306378_TRI.png
│ │ ├── chr22_1_20711065_FULL.pdf
│ │ ├── chr22_1_20711065_FULL.png
│ │ ├── chr22_1_20711065_TRI.pdf
│ │ └── chr22_1_20711065_TRI.png
│ └── target_beds
│ ├── chr13_1_22508596.bed
│ ├── chr14_1_17708411.bed
│ ├── chr15_1_22694466.bed
│ ├── chr21_1_16306378.bed
│ └── chr22_1_20711065.bed
├── plots
│ ├── contigs
│ │ ├── unique_sample_name_hap1.dist.log.png
│ │ ├── unique_sample_name_hap1.scatter.log.png
│ │ ├── unique_sample_name_hap2.dist.log.png
│ │ └── unique_sample_name_hap2.scatter.log.png
│ ├── ideo
│ │ └── minimap2
│ │ ├── unique_sample_name_to_CHM13.ideoplot.pdf
│ │ └── unique_sample_name_to_HG38.ideoplot.pdf
│ └── ploidy (only for CHM13)
│ └── CHM13
│ └── minimap2
│ ├── unique_sample_name.ploidy.pdf
│ └── unique_sample_name.summary.txt
├── saffire
│ ├── CHM13
│ │ ├── reference
│ │ │ ├── CHM13.fa
│ │ │ ├── CHM13.fa.fai
│ │ │ └── CHM13.genome.txt
│ │ └── results
│ │ ├── unique_sample_name_hap1
│ │ │ ├── alignments
│ │ │ │ └── unique_sample_name_hap1.minimap2.paf
│ │ │ └── beds
│ │ │ └── unique_sample_name_hap1.minimap2.bed
│ │ └── unique_sample_name_hap2
│ │ ├── alignments
│ │ │ ├── unique_sample_name_hap2.minimap2.bam
│ │ │ └── unique_sample_name_hap2.minimap2.paf
│ │ └── beds
│ │ └── unique_sample_name_hap2.minimap2.bed
│ └── HG38
│ ├── reference
│ │ ├── HG38.fa
│ │ ├── HG38.fa.fai
│ │ └── HG38.genome.txt
│ └── results
│ ├── unique_sample_name_hap1
│ │ ├── alignments
│ │ │ └── unique_sample_name_hap1.minimap2.paf
│ │ └── beds
│ │ └── unique_sample_name_hap1.minimap2.bed
│ └── unique_sample_name_hap2
│ ├── alignments
│ │ ├── unique_sample_name_hap2.minimap2.bam
│ │ └── unique_sample_name_hap2.minimap2.paf
│ └── beds
│ └── unique_sample_name_hap2.minimap2.bed
└── stats
├── seq_stats
│ ├── unique_sample_name_hap1.contig.stats
│ ├── unique_sample_name_hap1.scaftig.stats
│ ├── unique_sample_name_hap2.contig.stats
│ └── unique_sample_name_hap2.scaftig.stats
└── telo
├── unique_sample_name_hap1.contig.telo.tbl
├── unique_sample_name_hap1.scaftig.telo.tbl
├── unique_sample_name_hap2.contig.telo.tbl
└── unique_sample_name_hap2.scaftig.telo.tbl
- get_saf : saffire results including asm to ref paf
- get_compleasm : BUSCO results
- get_cleaned_fasta : Cleaned fasta
- get_stats : basic statistics such as N50
- get_qv: QV score
- get_plots : ploidy, projection, ModDot
./runcluster 30 get_qv get_compleasm
