Minimap2 generated a very large paf, and miniasm failed to get gfa, how to do with it ?

Question

[lovenlong]

Hi everyone,

I'm trying to assemble a plant genome (~400 Mb) with ONT data (SumBase ~20 Gb, 36.5k reads, mean len=53k). Due to some reasons, I have to do the assembly with my Desktop (i5-7400, 16 GB RAM, 2 TB disk).

I did overlap mapping with minimap2:

minimap2 -x ava-ont -k15 -Xw5 -m100 -g10000 -r2000 -t 2 -I 2G --max-chain-skip 25  ONT.fastq ONT.fastq > ONT.ovlap.paf

after ~70 hours, it finished and generated a PAF file with 689 GB in size.

then I tried to get gfa with miniasm (miniasm -f ONT.fastq ONT.ovlap.paf > ONT.gfa), but it failed due to core dump (Seg fault).

my questions are:

1. is it ok for the very large PAF resulted from minimap2 ?
2. how to calculate the PAF file size with a certain reads dataset ?
3. is possible to assemble my data just using 16 GB or 32 GB RAM ?

thanks

[WouterDeCoster]

I'd suggest you take a look at wtdbg2.

[lovenlong]

It works, thank you.

[colindaven]

Canu is also very good for long read assemblies