<![CDATA[BOL: FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads]]> https://bioinformaticsonline.com/bookmarks/view/37554/finishersca-repeat-aware-tool-for-upgrading-de-novo-assembly-using-long-reads? https://bioinformaticsonline.com/bookmarks/view/37554/finishersca-repeat-aware-tool-for-upgrading-de-novo-assembly-using-long-reads Mon, 20 Aug 2018 04:08:50 -0500 https://bioinformaticsonline.com/bookmarks/view/37554/finishersca-repeat-aware-tool-for-upgrading-de-novo-assembly-using-long-reads <![CDATA[FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads]]>
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

Address of the bookmark: https://github.com/kakitone/finishingTool

]]> Jit