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filter genome above N50 value

Hi everyone, I want to filter my assembly to get contigs above the N50 value only.

How can this be done.

--Thanks in advance

assembly
• 2,509 views • link
updated by Michael Dondrup Michael Dondrup • written by shubhra.bhattacharya shubhra.bhattacharya

You realize that your new filtered assembly will have a new, higher N50 value and you are just chasing a moving target until you have one contig left?

• 1 views • link
written by WouterDeCoster WouterDeCoster

1 answer

Calculate the N50 value, and extract all sequences with length >= N50 from your fasta file. The question is just, why? N50 is not a magical threshold below which contigs are not real.

• 1 views • link
written by Michael Dondrup Michael Dondrup

Hi! I have two genomes (both draft) of an organism. I have to find out which genome between these two has to be used as a reference for my downstream analysis (transcriptome and SNP profile study etcc) For this genome-genome comparison I have used approaches such as synmap, LAST and mauve but I still cannot reach a conclusion. So, that is the reason I am wanting to filter them at N50 and see where it goes. Kindly suggest any other alternatives as well if possible.

--Thanks in advance

• 1 views • link
written by shubhra.bhattacharya shubhra.bhattacharya

Have you tried to check if you can reconcile the two assemblies to see if you can make a better combined one?

• 1 views • link
written by GenoMax GenoMax

There are many:

  • remapping completeness of DNA/RNA seq
  • linkage map - linkage errors
  • BUSCO
  • estimate of contamination, e.g. by bacterial contigs
  • repeat rate, GC content, assembly size vs. expected values
  • ....
• 1 views • link
written by Michael Dondrup Michael Dondrup

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