DeNovo

cd
sudo apt install gnuplot --fix-missing
mv /home/manager/miniconda/bin/mummerplot /home/manager/miniconda/bin/mummerplot-old
sed '1154d' /home/manager/miniconda/bin/mummerplot-old > /home/manager/miniconda/bin/mummerplot
chmod +x /home/manager/miniconda/bin/mummerplot
git clone https://github.com/vbsreenu/ContigsMerger.git
sudo chmod -R 777 /usr/local/lib/python2.7/dist-packages/quast_libs/bedtools



cd ~/DeNovo/SARS-CoV-2
gunzip *.gz
trim_galore --length 75 -q 30 --paired --illumina SARS-CoV2_1.fq SARS-CoV2_2.fq
mkdir Spades IDBA_UD Abyss


cd ~/DeNovo/SARS-CoV-2/Spades
spades.py --careful -k 21,53,97 -1 ../SARS-CoV2_1_val_1.fq -2 ../SARS-CoV2_2_val_2.fq -o .


cd ~/DeNovo/SARS-CoV-2/IDBA_UD/
fq2fa --merge --filter ../SARS-CoV2_1_val_1.fq ../SARS-CoV2_2_val_2.fq reads.fa
idba_ud --mink=45 --maxk=75 step=5 -r reads.fa -o idba_ud


cd ~/DeNovo/SARS-CoV-2/Abyss/
abyss-pe k=27 n=4 in='../SARS-CoV2_1_val_1.fq ../SARS-CoV2_2_val_2.fq' name=Abyss

for k in $(seq 45 5 75);
do
  abyss-pe k=$k n=4 in='../SARS-CoV2_1_val_1.fq ../SARS-CoV2_2_val_2.fq' name=Abyss-$k;
done

abyss-fac *-contigs.fa

cd ~/DeNovo/GapFilling/
gunzip SRR14547043*

trim_galore --length 75 -q 30 --paired --illumina SRR14547043_1.fastq SRR14547043_2.fastq
mkdir Spades IDBA_UD Abyss
cd Spades/
spades.py --careful -k 27,53,71 -1 ../SRR14547043_1_val_1.fq -2 ../SRR14547043_2_val_2.fq -o .

cd ~/DeNovo/GapFilling/IDBA_UD/
fq2fa --merge --filter ../SRR14547043_1_val_1.fq ../SRR14547043_2_val_2.fq reads.fa
idba_ud --mink=25 --maxk=75 step=7 -r reads.fa -o idba_ud
cd ~/DeNovo/GapFilling/Abyss/
for k in $(seq 25 7 95);
do
  abyss-pe k=$k n=4 in='../SRR14547043_1_val_1.fq ../SRR14547043_2_val_2.fq' name=Abyss-$k;
done
abyss-fac *-contigs.fa




cd ~/DeNovo/
mkdir Ref
cd Ref
wget -O SARS-CoV-2.fa https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore\&id=NC_045512\&rettype=fasta\&retmode=text
wget -O SARS-CoV-2.gff https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore\&id=NC_045512\&rettype=gff\&retmode=text

cd ~/DeNovo/
mkdir Validate
cd Validate
nucmer ../Ref/SARS-CoV-2.fa ../GapFilling/Spades/contigs.fasta  -p Spades
mummerplot -p Spades -t png Spades.delta
eog Spades.png

cat ../GapFilling/Abyss/*-contigs.fa > Abyss-contigs.fa

=========
RUN THIS COMMAND TO FIX THE PERMISSION ERROR WHILE RUNNING QUAST

sudo chmod -R 777 /usr/local/lib/python2.7/dist-packages/quast_libs/bedtools
=========

quast.py -l "Spades, IDBA, Abyss" ../GapFilling/Spades/contigs.fasta ../GapFilling/IDBA_UD/idba_ud/contig.fa  Abyss-contigs.fa -R ../Ref/SARS-CoV-2.fa --genes ../Ref/SARS-CoV-2.gff  --reads1 ../GapFilling/SRR14547043_1_val_1.fq --reads2 ../GapFilling/SRR14547043_2_val_2.fq

cd quast_results/latest
firefox report.html




cd ~/DeNovo/GapFilling/
cat Abyss/*-contigs.fa Spades/contigs.fasta IDBA_UD/idba_ud/contig.fa > all_contigs.fa
~/ContigsMerger/contigsMerger ../Ref/SARS-CoV-2.fa all_contigs.fa N

~/ContigsMerger/contigsMerger ../Ref/SARS-CoV-2.fa all_contigs.fa