Spades - commandline
This tutorial follows on from “PacBio assembly with commandline tools”.
Short-read assembly: a comparison
So far, we have assembled the long PacBio reads into one contig (the chromosome) and found an additional plasmid in the Illumina short reads.
If we only had Illumina reads, we could also assemble these using the tool Spades.
You can try this here, or try it later on your own data.
We will use the same Illumina data as we used above:
illumina_R1.fastq.gz: the Illumina forward reads illumina_R2.fastq.gz: the Illumina reverse reads
This is from Sample 25747.
spades.py -1 illumina_R1.fastq.gz -2 illumina_R2.fastq.gz --careful --cov-cutoff auto -o spades_assembly_all_illumina
-1is input file of forward reads
-2is input file of reverse reads
--carefulminimizes mismatches and short indels
--cov-cutoff autocomputes the coverage threshold (rather than the default setting, “off”)
-ois the output directory
Move into the output directory and look at the contigs:
Run “Prokka” to annotate the contigs.