Question: Minimap2 generated a very large paf, and miniasm failed to get gfa, how to do with it ?
gravatar for lovenlong
8 months ago by
lovenlong10 wrote:

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 ?


assembly genome • 545 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by lovenlong10

I'd suggest you take a look at wtdbg2.

ADD REPLYlink written 8 months ago by WouterDeCoster42k

It works, thank you.

ADD REPLYlink written 8 months ago by lovenlong10

Canu is also very good for long read assemblies

ADD REPLYlink written 8 months ago by colindaven1.8k
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