Here is the command to run the tool:
python finisherSC.py destinedFolder mummerPath
If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.
python finisherSC.py -par 20 destinedFolder mummerPath
Sometimes, if the names of raw reads and contigs consists of special characters/formats, FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command.
perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' raw_reads.fasta > newRaw_reads.fasta
cp newRaw_reads.fasta raw_reads.fasta
perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' contigs.fasta > newContigs.fasta
cp newContigs.fasta contigs.fasta