<![CDATA[BOL: My commonly used commands in Bioinformatics]]> https://bioinformaticsonline.com/pages/view/37411/my-commonly-used-commands-in-bioinformatics? https://bioinformaticsonline.com/pages/view/37411/my-commonly-used-commands-in-bioinformatics Thu, 26 Jul 2018 04:58:45 -0500 https://bioinformaticsonline.com/pages/view/37411/my-commonly-used-commands-in-bioinformatics <![CDATA[My commonly used commands in Bioinformatics]]> FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually:

minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta racon_assembly.fasta
nucmer -p nucmer assembly.fasta racon_assembly.fasta
show-snps -C -T -r nucmer.delta

This reports Racon's changes in a table. You can exclude indels with the -I option in show-snps. 

This process (Racon -> MUMmer -> SNP table) solves the problem I originally raised in this issue. So as far as I'm concerned, you can close this issue (or keep it open if you still want to implement some kind of variant table).

]]> Rahul Nayak