Part 3: Single cell genome assembly

3.4. Assessing assembly quality using Quast

After assembling the reads into contigs, you will use this tool called ‘Quast’ to calculate the basic metrics such as the length of largest contig, N50, etc.
To run ‘Quast’, first we will create a link to the different contig files in the assembly folder. Use the following commands to help yourself:

cd assemblies
ln -s `pwd`/IDBA${trim}/contig.fa G5_${sample}${trim}_IDBA_contig.fasta
ln -s `pwd`/Spades${trim}/contigs.fasta G5_${sample}${trim}_Spades_contig.fasta
ln -s `pwd`/Ray${trim}/Contigs.fasta G5_${sample}${trim}_Ray_contig.fasta

then run quast on all assemblies at once:

quast.py -T 8 -o assembly_metrics *.fasta

Results from ‘Quast’ will be found in the assembly_metrics folder. Take a look at the files produced by the program. The summary file containing the stats is report.txt. You should see the assembly metrics such as N50, G+C%, largest contig, total length (i.e., total length of all contigs added).

Report the results in the spreadsheet:

less assembly_metrics/report.txt