Hey friends!
I have a large number of fastq files of COVID-19 from GridION sequencing,
I want to produce FASTA files of the assembly results.
because the size of the reads is large (about 800-1200 bases) TRINITY didn't work well for me.
what other tools can I use to assembly these files??
BTW: I was able to produce BAM sorted files using MINIMAP2 but I need the assembly results.
It looks like you don't have enough data for assembly, not that flye does not work. Follow the link above, for getting a consensus sequence from the data you have aligned using minimap2.
thanks! I installed Flye, but it yields an error:
I checked in BLAST to see if there is an overlap and there is
Does not look like you have much coverage (at least in that file) if the log above is to be believed.
You may want go the alignment and call consensus route if you don't have enough data for assembly.
look like Flye, didn't work for viruses. what tool is good for alignment? I need to get a sequence
It looks like you don't have enough data for assembly, not that
flye
does not work. Follow the link above, for getting a consensus sequence from the data you have aligned usingminimap2
.