create plurality consensus from 24 reference genomes

[ammaraziz]

To create the plurality consensus:

1. Reference genomes were oriented with dnaapler

   for f  in *.fasta; do echo $f; dnaapler all -i $f -o plurality/${f/.fasta/.reorient} -t 6; done

2. Aligned with all-to-all mugsy default settings on the output of dnaapler

   mugsy -p mugsyout *.fasta

3. Each region (separated by =) is extracted manually
4. For each region goalign consensus is run:

   goalign consensus --ignore-gaps -i input.fasta -o output.cons.fasta

5. Concat all cons.fa sequences and rename:

   cat *.cons.fa | seqkit replace -p "$" -r "_{nr}" > plurality_all.fasta

6. All plurality consensus was scaffolded against Ct Genotype D using ragtag:

   ragtag.py scaffold -u scaffoldReference.fasta plurality_all.fasta -o plurality_1_scaffold

7. Output is renamed again:

seqkit replace -p "(.*)" -r "plurality_{nr}" plurality_scaffold/ragtag.scaffold.fasta > plurality_final.fasta

plurality_final.txt

[ammaraziz]

all.reoriented.txt