assembly of contigs into scaffolds

Question

[M.Nadeem Khan]

Hello All.. I sequenced a fungal genome, assembled it into reads and then into contigs, then I tried to annotate it through RAST but it did not proceed and the command was "your sequence has more contigs and cannot be processed" the number of contigs is exceeding 1000. the size is 23MB. Is there any tool automated online tool which can assemble it into large-sized contigs or scaffolds? As for the time being, I need it on urgent basis. Thank you for your cooperation.

Answer 1

[shubhra.bhattacharya]

Hi! Few questions first: 1)What do you mean when you say "assembled into reads". 2)Also what reads are these (Long reads,short reads etc?) 3)Are you processing your reads in any way?

I have done fungal assembly of 150X2 reads (150 bases,Paired end) using SPAdes and I got satisfactory results.

[M.Nadeem Khan]

Dear thank you for your response. these are 1500 short reads. I want to process these reads. I just want to annotate these

[shubhra.bhattacharya]

Usually reads will have adapter sequences in them which may be removed prior to assembly (Tools like cutadapt etc are available for the same).

https://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/ for more info on different assemblers.

Meanwhile many tutorials for WGS assembly is available online as well.

Since this will be a de-novo assembly many gene prediction tools etc are available such as Augustus,Genemark etc for gene prediction.