Assembly Quality Assessment and Protein Prediction

Why We Need Assembly Quality Assessment

• Understand the quality of data obtained from assembling with MEGAHIT.
• Do not overly trust your tools; fully understand your data.

How to Know Our Contigs Data

BUSCO

• Install BUSCO using conda:

conda activate envname
conda install -c conda-forge -c bioconda busco=5.3.2

• Run BUSCO:

busco -i genome.fa -c 10 -o outputdir -m geno/prot/tran -l refdatabase_path --offline

• Get your reference database from: BUSCO Data

QUAST

• Install QUAST using conda:

conda activate envname
conda install quast

• Basic usage:

quast.py contigs.fas

• More sophisticated usage:

quast.py contigs_1.fa contigs_2.fa -r reference.fa -g genome.gff -1 reads1.fastq.gz -2 reads2.fastq.gz -o quast_out -t 12

• QUAST can run without a reference genome, but there will be no gene alignment information.

getorf

• Install EMBOSS to use getorf:

conda install -c bioconda emboss

• Command example:

getorf -minsize 600 -sequence input.fna -outseq output.faa

• getorf extracts Open Reading Frames (ORFs) from a nucleotide sequence and translates them into protein sequences.