Hybridassemblies
- the currently to go standard is nanopore and illumina reads combined
- this is easily done via unicycler
- github link
What it does (briefly):
spades Assembly with illumina reads only
closing the gaps using only the nanopore Reads
polishing via pilon
and a few more corrections and stuff
* So we only go with porechop for long reads and scythe sickle for short reads
Unicycler
unicycler -1 <fwd>_R1.fastq.gz -2 <rev>_R2.fastq.gz -l nanopore_reads.fastq -o outputfolder
-1 and -2 are the illumina inputs -l is the long read input -o is the output
Assembly visualization
- with
BandageBandage is a GUI to interact with assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others.
Figure: Connects Contigs; Repeats are region were many contigs connect; nanopore is one line