Hi everyone, I want to filter my assembly to get contigs above the N50 value only.
How can this be done.
--Thanks in advance
Hi everyone, I want to filter my assembly to get contigs above the N50 value only.
How can this be done.
--Thanks in advance
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.
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
There is "newer" pipeline for combining the two assemblies called NucMerge that you might try (https://www.biorxiv.org/content/early/2018/11/30/483701), but I would first consider C: filter genome above N50 value
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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?