search

christophertbrown / iRep

scripts for estimating bacteria replication rates based on population genome copy number variation
MIT License
68 stars 9 forks source link

Using GC Skew to reorder contigs #37

Open balags1 opened 3 years ago

balags1 commented 3 years ago

It is very useful to know Ori/Ter in draft genomes. However, is there a way to reorder multiple non-overlapping contigs then, such as from a WGS Illumina sequencing experiment yielding a 30-100 contigs assembly, to match appropriate GC Skew distribution? To do this independently based on the GC skew distribution, without a reference genome?

christophertbrown commented 3 years ago

This is a good question, and agree knowing Ori/Ter can be helpful. We considered this, but found that the signal was too low and the number of possible configurations too great in most cases. If you have a genome in very few piece (e.g. 2-5), it can be helpful.

Chris

On Jun 21, 2021, at 7:31 PM, balags1 @.***> wrote:

 It is very useful to know Ori/Ter in draft genomes. However, is there a way to reorder multiple non-overlapping contigs then, such as from a WGS Illumina sequencing experiment yielding a 30-100 contigs assembly, to match appropriate GC Skew distribution?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.