current protocols synteny

prepare.sh

export OUT=/var/www/html/jbrowse2
## download and unzip NCBI genomes
datasets download genome accession GCF_000307795.1 --include gff3,genome --filename h_pylori_j99.zip
datasets download genome accession GCF_000982695.1 --include gff3,genome --filename h_pylori_26695.zip
unzip -o h_pylori_j99.zip
unzip -o h_pylori_26695.zip
cd ncbi_dataset/data
mv GCF_000982695.1/GCF_000982695.1_ASM98269v1_genomic.fna h_pylori_j99.fa
mv GCF_000307795.1/GCF_000307795.1_ASM30779v1_genomic.fna h_pylori_26695.fa

## index FASTA files with "samtools faidx"
samtools faidx h_pylori_26695.fa
samtools faidx h_pylori_j99.fa

## load indexed FASTA files into jbrowse
jbrowse add-assembly h_pylori_26695.fa --out $OUT --load copy
jbrowse add-assembly h_pylori_j99.fa --out $OUT --load copy

## minimap2 based whole genome alignment
minimap2 -c h_pylori_26695.fa h_pylori_j99.fa > 26695_vs_j99.paf
jbrowse make-pif 26695_vs_j99.paf
jbrowse add-track 26695_vs_j99.pif.gz -a h_pylori_j99,h_pylori_26695 --out $OUT --load copy

## create tabix-indexed gff3 for gene annotations
jbrowse sort-gff GCF_000307795.1/genomic.gff | bgzip > h_pylori_26695.gff.gz
jbrowse sort-gff GCF_000982695.1/genomic.gff | bgzip > h_pylori_j99.gff.gz
tabix h_pylori_j99.gff.gz
tabix h_pylori_26695.gff.gz

# load gene annotations
jbrowse add-track h_pylori_26695.gff.gz --out $OUT --load copy -a h_pylori_26695
jbrowse add-track h_pylori_j99.gff.gz --out $OUT --load copy -a h_pylori_j99

## create text index for gene name searching
jbrowse text-index --out $OUT