I've performed a de novo assembly of a bacterial genome using SPAdes, and now want to use Bandage to visualise the assembly. The input file for Bandage is a .paths file.
I'm using the latest version of SPAdes (3.7.1), and in the manual (http://spades.bioinf.spbau.ru/release3.7.1/manual.html#sec3.5) it says that it should generate .paths files of the contigs and scaffolds.
The problem is that after performing the assembly using SPAdes, there are no .paths files present in the output directory. Does anyone know why they might not be produced, or how to get them?
The command I used assemble the genome using SPAdes was:
spades.py --careful -1 file1.fq -2 file2.fq -o assembly.spades
I haven't used bandage but a look at the github site: (https://rrwick.github.io/Bandage/) says that it uses the FASTG file which I know is produced by the spades assembly.
Yes I have used .fastg output file created by SPAdes. Try it, it will work
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