# Creation of a new branch
git checkout -b MSA_error
There is a problem in the C-NR-genome, the 'N' may not correspond to mismatches but insteed to the absence of MSA upstream of the EMBOSS cons
. I will therefore proceed to a multiple alignment and a cunt from the genomes assembled
# conda create -c bioconda -y -n mafft mafft
# conda create -c bioconda -y -n emboss emboss
# conda create -c bioconda -y -n mummer4 mummer4
# MSA
conda activate mafft
cat *.fasta >> oshv.fna
mafft \
--thread 4 \
--auto \
oshv.fna \
> oshv.faa
conda deactivate
# Generate consensus
conda activate emboss
cons -sequence oshv.faa \
-outseq C-NR-genome.fasta \
-plurality 0.2 -name C-NR-genome.fasta
conda deactivate
# WG comparison
conda activate mummer4
NR_genomes_seq=oshv.fna
Consensus_global=C-NR-genome.fasta
# mumref
nucmer -c 100 -l 15 -f -p nucmer_numref $Consensus_global $NR_genomes_seq
show-coords -r -c -l nucmer_numref.delta > nucmer_numref.coords
show-snps -T nucmer_numref.delta > nucmer_numref.snps
conda activate mafft
mafft --addfragments C-NR-genome.fasta oshv.faa >> oshv_and_C-NR.faa