An example pipeline for running SyRI

Set variables

cwd="."     # Change to working directory
PATH_TO_SYRI="../syri/bin/syri" #Change the path to point to syri executable
PATH_TO_PLOTSR="../syri/bin/plotsr" #Change the path to point to plotsr executable

Got to the working directory and downloand the Yeast reference genome and a query assembly

cd $cwd
## Get Yeast Reference genome
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/146/045/GCA_000146045.2_R64/GCA_000146045.2_R64_genomic.fna.gz
## Get Query genome
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/977/955/GCA_000977955.2_Sc_YJM1447_v1/GCA_000977955.2_Sc_YJM1447_v1_genomic.fna.gz

Unzip the pre-process the genome

gzip -df GCA_000146045.2_R64_genomic.fna.gz
gzip -df GCA_000977955.2_Sc_YJM1447_v1_genomic.fna.gz
## Remove mitochondrial DNA
head -151797 GCA_000977955.2_Sc_YJM1447_v1_genomic.fna > GCA_000977955.2_Sc_YJM1447_v1_genomic.fna.filtered
ln -sf GCA_000146045.2_R64_genomic.fna refgenome
ln -sf GCA_000977955.2_Sc_YJM1447_v1_genomic.fna.filtered qrygenome

Note

Ideally, syri expects that the homologous chromosomes in the two genomes would have exactly same chromosome id. Therefore, it is recommended that the user pre-processes the fasta files to ensure that homologous chromosomes have exactly the same id in both fasta files corresponding to the two genomes. In case, that is not the case, syri would try to find homologous genomes using whole genome alignments, but that method is heuristical and can result in suboptimal results. Also, it is recommended that the two genomes (fasta files) should have same number of chromosomes.

Perform whole genome alignment

# Using minimap2 for generating alignment. Any other whole genome alignment tool can also be used.
minimap2 -ax asm5 --eqx refgenome qrygenome > out.sam

Note

It is recommended that the user tests different alignment settings to find what alignment resolution suits their biological problem. Some alignment tools find longer alignments (with lots of gaps) while other find smaller more fragmented alignments. The smaller alignments generally have higher alignment identity scores and are more helpful in identifying smaller genomic structural rearrangments. But they could also lead to significant increase in redundant alignments which leads to increase in runtime of the alignment tool and SyRI.

Ryn SyRI

python3 $PATH_TO_SYRI -c out.sam -r refgenome -q qrygenome -k -F S

samtools view -b out.sam > out.bam
python3 $PATH_TO_SYRI -c out.bam -r refgenome -q qrygenome -k -F B

SyRI would report genomic structural differences in syri.out and syri.vcf.

Plotting genomic structures predicted by SyRI

python3 $PATH_TO_PLOTSR syri.out refgenome qrygenome -H 8 -W 5

Using SyRI to identify genomic rearrangements from whole-genome alignments generated using MUMmer

nucmer --maxmatch -c 100 -b 500 -l 50 refgenome qrygenome       # Whole genome alignment. Any other alignment can also be used.
delta-filter -m -i 90 -l 100 out.delta > out.filtered.delta     # Remove small and lower quality alignments
show-coords -THrd out.filtered.delta > out.filtered.coords      # Convert alignment information to a .TSV format as required by SyRI
python3 $PATH_TO_SYRI -c out.filtered.coords -d out.filtered.delta -r refgenome -q qrygenome
python3 $PATH_TO_PLOTSR syri.out refgenome qrygenome -H 8 -W 5