Question: Minimap2 generated a very large paf, and miniasm failed to get gfa, how to do with it ?
1
gravatar for lovenlong
5 weeks ago by
lovenlong10
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 ?

thanks

assembly genome • 140 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by lovenlong10

I'd suggest you take a look at wtdbg2.

ADD REPLYlink written 5 weeks ago by WouterDeCoster37k

It works, thank you.

ADD REPLYlink written 4 weeks ago by lovenlong10

Canu is also very good for long read assemblies

ADD REPLYlink written 24 days ago by colindaven1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 889 users visited in the last hour