Complete-mitochondrial-genome-analysis/script at main · BariSayed/Complete-mitochondrial-genome-analysis · GitHub

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# Install core tools for mtDNA assembly and analysis
conda install -c bioconda -c conda-forge \
  fastqc \
  trimmomatic \
  bwa \
  samtools \
  bcftools \
  getorganelle \
  spades \
  seqtk \
  sra-tools \
  blast \
  -y

# For visualizing assemblies
conda install -c bioconda bandage -y
# For phylogenetic analysis or downstream annotation
conda install -c bioconda mafft muscle -y

# Trimming with Trimmomatic
# Download the TruSeq3-PE-2.fa adapter
wget https://github.com/timflutre/trimmomatic/raw/master/adapters/TruSeq3-PE-2.fa

trimmomatic PE -phred33 -threads 12 \
  SRR30436367_1.fastq SRR30436367_2.fastq \
  SRR30436367_trimmed_1P.fq SRR30436367_trimmed_1U.fq \
  SRR30436367_trimmed_2P.fq SRR30436367_trimmed_2U.fq \
  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 \
  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

# Denovo genome assembly
# Run GetOrganelle
get_organelle_from_reads.py -h # Check software working

get_organelle_from_reads.py \
  -1 SRR30436367_trimmed_1P.fq \
  -2 SRR30436367_trimmed_2P.fq \
  -o getorganelle_output \
  -R 15 \
  -k 21,45,65,85,105 \
  -F animal_mt \
  -t 12

# SPAdes de novo Assembly of mtDNA
spades.py \
  -1 SRR30436367_trimmed_1P.fq \
  -2 SRR30436367_trimmed_2P.fq \
  -o spades_mt_output \
  -t 12 \
  --only-assembler