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bhattlab / lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

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Lathe Assembly Binning

saras224 opened this issue · comments

commented

Hi @elimoss
I am using your tool for assembling my long reads metagenome. I have a doubt in the procedure of assembly that does the lathe also bin the genomes before doing the circularization or do we have to do it separately after obtaining the final contig after the assembly is completed?
And I have few more questions that I wanted to ask:

Why are you using the very outdated version of FLYE assembler when they have upgraded to better versions where we don't have to give the genome sizes as they have told me?

I have done assembly of long read (ONT) using lathe and I do not see a very good result. The largest contig was of length 1130359. My sample is a diverse wastewater sample and I expect the largest contig to be much higher and of course, should be more in number as these have millions of bacteria and the minimum genome size of a bacteria should be more than 0.5 mega base pairs.

What parameters can be changed to achieve a better assembly result other than genome size? What genome size I should provide when I am expecting my sample to be diverse. I gave 100m and 250m, should I increase the genome size to 2500m and 4500m?

Thanks
Saraswati Awasthi

commented

Hello Saraswati Awasthi
I am processing some long reads metagenome ,too . But from the workflow of Lathe , i don"t how can get the bins from the metagenome. Have u solve your problems from using this workflow ?

Thanks
Binghe Zhao