5. Evaluating output¶

When we ran PGGB, the 'odgi stats -S' option was utilized to generate statistics for both the seqwish and smoothxg graphs and the 'multiqc -m' option was employed to generate a MultiQC report, providing comprehensive statistics and visualizations of the graphs. All pertinent results can be located in the MultiQC report, which is saved in HTML format.
The output folder contains all the PGGB-related results, including the .smooth.final.og and all associated visualization figures. It also includes .final.smooth.gfa (a Graphical Fragment Assembly file), as well as variations of the graph presented in a VCF (Variant Call Format) file

check the files¶

code

cd  ~/pg_workshop/5NM_2Kb94

ls

Output

5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.07-24-2023_10:49:02.log         
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.07-24-2023_10:49:02.params.yml  
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.gfa                       
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.NC_017518.1.vcf           
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.NC_017518.1.vcf.stats     
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og                        
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.lay                    
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.lay.draw_multiqc.png   
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.lay.draw.png           
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.lay.tsv                
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.stats.yaml             
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.viz_depth_multiqc.png
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.viz_inv_multiqc.png
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.viz_multiqc.png
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.viz_O_multiqc.png
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.viz_pos_multiqc.png
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.final.og.viz_uncalled_multiqc.png
5NM.fa.fefc7f5.417fcdf.e2ae00b.smooth.fix.affixes.tsv.gz
5NM.fa.fefc7f5.417fcdf.seqwish.og.stats.yaml
5NM.fa.fefc7f5.alignments.wfmash.paf
multiqc_config.yaml
multiqc_data
multiqc_report.html

check the .gfa file.¶

(Graphical Fragment Assembly) GFA is a file format commonly used to represent assembly graphs or sequence variation graphs

code

head 5NM*.gfa |less -S

Output

H       VN:Z:1.0
S       1       ATCCGCCCGACCAAGAAGGCATTTTGGAACTACACATCCGCAGGCGCAAAAACGGTGTCTGCTCGGAAATGATTTTCGGCAGCGAACCCAAAGTCAAAGAAAAAGGCATCGTCCG
L       1       +       4       +       0M
S       2       CGAAATTGTTTCTTTGTCCGTTTGCGATGTTTTTTAGCTTTGGGGCAGTCGAGAATCACGCCGCTCGTTCGGCTTGTGTAACTGATGTTTTTATGCCCCCTTATCTAACAGGGGG
L       2       +       133478  +       0M
S       3       TCCATTGGGGCAAGGCCGCCGCGCCGACCGGTTTGGCTTCCCACACTTCCCCCTTTGCCGCCAATGCGGCAAACCATTTGGACTGGAGCTGGGTTTTCTCCAGTTTGGGCAGCAA
L       3       +       175915  +       0M
S       4       G
L       4       +       5       +       0M
S       5       CCATCGGACGCTTGGACATCAACACCAGCGGACTTCTGATTCT

tail 5NM*.gfa |less -S

output

S       246216  G
L       246216  +       246135  +       0M
L       246216  +       246217  +       0M
S       246217  GAC
L       246217  +       246136  +       0M
P       NC_003112.2     85316+,85318+,85319+,85321+,85322+,85323+,85325+,85327+,85328+,85330+,85331+,85333+,85334+,85336+,85337+,85
P       NC_017518.1     85316+,85317+,85319+,85320+,85322+,85323+,85325+,85326+,85328+,85329+,85331+,85332+,85334+,85335+,85337+,85
P       NZ_CP007668.1   1+,4+,5+,6+,8+,9+,11+,12+,14+,15+,17+,18+,20+,21+,23+,25+,26+,27+,29+,31+,32+,34+,35+,37+,38+,39+,41+,43+,4
P       NZ_CP016880.1   2+,133478+,133479+,133481+,133482+,133483+,133485+,133486+,133488+,133489+,133490+,133492+,133493+,133495+,
P       NZ_CP020423.2   3+,175915+,175916+,175918+,175919+,175921+,175922+,175924+,175925+,175926+,175928+,175929+,175931+,175932+,

what does S, L, P mean

S means DNA segments, L means links between notes, and P means paths

Pangenome graph visualization using ODGI¶

ODGI Compressed 1D visualization¶

This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. Summarization of path coverage across all paths. Dark blue means highest coverage. Dark red means lowest coverage. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.