Use the most popular assembler SPAdes to assemble a bacterial genome.


conda install spades


When using SPAdes it is typical to choose at least 3 k-mer sizes. One low, one medium and one high. We will use 33, 55 and 91.

First merge the unpaired reads

cd seqtk
cat SRR10561173_2U_seqtk.fastq.gz >> SRR10561173_1U_seqtk.fastq.gz
rm SRR10561173_2U_seqtk.fastq.gz
mv SRR10561173_1U_seqtk.fastq.gz SRR10561173_U_seqtk.fastq.gz
cd ..

then run spades -1 ~/seqtk/SRR10561173_1P_seqtk.fastq.gz -2 ~/seqtk/SRR10561173_2P_seqtk.fastq.gz -s ~/seqtk/SRR10561173_U_seqtk.fastq.gz -k 33,55,91 -o ~/assembly

Check the result.

File content
contigs.fasta assembled contigs
scaffolds.fasta assembled scaffolds
assembly_graph.fastg the graph of contigs
assembly_graph_with_scaffolds.gfa the graph of scaffolds
spades.log the log file of the spades running

Quanlity assessment of the assembly

  • Install quast and bandage

    quast have some compatibility problem with the bioinfo environment, the solution is to install it in a separate environment.

      conda create -n quast
      conda activate quast
      conda install quast
  • Run quast

    quast use a reference to assess the quality of the assembly. Upload the reference genome and annotation file salmonella_typhimurium_lt2.fasta and salmonella_typhimurium_lt2.gff to the server.

      quast ~/assembly/SRR10561173.fasta -R ~/seq/salmonella_typhimurium_lt2.fasta -G ~/seq/salmonella_typhimurium_lt2.gff -o ~/quast/

    Check the result.

  • Run bandage

    Download and install bandage from bandage website, or copy from my folder.

    Download the FASTG graph file of SPAdes to your laptop, open it with bandage.