example

Toy example

Here we present a walkthrough of running pandora on a toy example. We run:

1. pandora without de novo discovery;
2. pandora with de novo discovery (see Figure 2 of our paper).

Dependencies

• There is no need to have pandora or make_prg installed. The running script will automatically download and run the precompiled binaries;
• MAFFT has to be in your PATH in order to run make_prg update. It can be installed:
  1. from source: https://mafft.cbrc.jp/alignment/software/;
  2. using conda: conda install -c bioconda mafft;
• wget;
• make_prg requirements: GLIBC >= 2.17 (present on Ubuntu >= 13.04, Debian >= 8.0, CentOS >= 7, RHEL >= 7.9, Fedora >= 19, etc);

Input data description

• msas/ : contains the MSAs of the two genes we are using as toy example here, GC00006032 and GC00010897;
• reads/ : contains 100x of perfect simulated reads from two toy samples. We simulated perfect reads, where one sample genotypes to one allele of the variant sites, while the other sample genotypes towards the other allele;

Running

./run_pandora.sh

Quick look at the output

prgs: contains output of make_prg from_msa and pandora index. Main files:

• pangenome.prg.fa: the PRG itself;
• pangenome.prg.fa.k15.w14.idx and kmer_prgs: the PRG index;
• pangenome.update_DS: update data structures that make the PRG updateable;

pandora_discover_out: contains the output of pandora discover. Main files:

• denovo_paths.txt: describes the denovo paths found in all samples;

updated_prgs: contains the output of make_prg update and pandora index (on the updated PRG). The files are similar to the ones in the prgs folder;

output_toy_example_no_denovo and output_toy_example_with_denovo: contains the output of pandora compare without denovo discovery and with denovo discovery, respectively. Main files:

• pandora_multisample.matrix: see https://github.com/rmcolq/pandora/wiki/FAQ#q-where-can-i-find-gene-presenceabsence-information ;
• pandora_multisample.vcf_ref.fa: see https://github.com/rmcolq/pandora/wiki/FAQ#q-what-are-the-sequences-in-pandora_multisamplevcf_reffa
• pandora_multisample_genotyped.vcf: the VCF file containing variants for all samples;

Looking at the genotyped VCFs

No denovo

Taking a quick look at an excerpt of output_toy_example_no_denovo/pandora_multisample_genotyped.vcf (the VCF genotyped by pandora without denovo sequences):

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	toy_sample_1	toy_sample_2
GC00006032	146	.	T	C	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	1:0,41:0,52:0,41:0,52:0,83:0,105:1,0:-526.281,-18.7786:507.502	0:15,0:15,0:15,0:15,0:31,0:31,0:0,1:-3.53065,-214.155:210.624
GC00006032	160	.	A	C	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	1:0,26:0,40:0,33:0,50:0,106:0,160:1,0.25:-401.941,-17.9221:384.019	0:19,0:12,0:19,0:12,0:38,0:24,0:0,1:-3.32705,-218.76:215.433
GC00006032	218	.	T	C	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	1:3,11:4,14:0,11:0,14:12,23:16,28:0.75,0:-182.162,-41.9443:140.217	0:11,0:5,0:13,0:6,0:44,0:21,0:0.25,1:-19.9705,-149.683:129.712

We can see samples toy_sample_1 and toy_sample_2 genotype towards different alleles.

With denovo

The VCF (output_toy_example_with_denovo/pandora_multisample_genotyped.vcf) has some new variants that were discovered and genotyped. For example:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	toy_sample_1.100x.random.illumina	toy_sample_2.100x.random.illumina
GC00006032	49	.	A	G	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	0:44,0:59,0:44,0:59,0:44,0:59,0:0,1:-26.8805,-570.333:543.452	1:0,48:0,50:0,48:0,50:0,97:0,100:1,0:-537.307,-28.9415:508.365
GC00010897	44	.	C	T	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	1:0,11:0,16:0,11:0,16:0,23:0,32:1,0:-220.34,-8.03511:212.304	0:22,0:18,0:22,0:18,0:44,0:37,0:0,1:-2.87264,-270.207:267.334
GC00010897	422	.	A	T	.	.	SVTYPE=SNP;GRAPHTYPE=SIMPLE	GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF	1:0,8:0,5:0,8:0,5:0,16:0,11:1,0:-155.867,-20.2266:135.641	0:12,0:9,0:12,0:9,0:12,0:9,0:0,1:-9.39494,-182.709:173.314