Question: how to set a quality value for each contig in a NGS assembly
gravatar for lessismore
5.5 years ago by
lessismore880 wrote:

Dear all,

i would like to relate the coverage of a contig, resulted from a NGS sequencing, to its length and relate this value to the genome length for comparing quality of contigs for different assemblies and in the end the quality of each assembly in genera.

for exemple:

for a genome 150kb in legth there are 3 different genotypes sequenced (lets call them a,b,c), each one with a set of contigs.

contig1a: coverage 1000x and length 50kb

could be much more useful than

contig1b: coverage 200x and length 50kb

and than

contig1c: coverage1000x and length 1kb

where contig1a, contig1b, contig1c belong to 3 different genotypes and so to different assemblies.

i know the parameter NG50 but i want to relate this parameter to the coverage and set a quality value for each contig, which for me is very important.

Anyone can help?

Thanks in advance

next-gen assembly genome • 1.7k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 5.5 years ago by lessismore880
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