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lh3 / miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)
MIT License
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empty .gfa #47

Open Raistrawby opened 6 years ago

Raistrawby commented 6 years ago

Hello, I would like to assemble my MinIon output (fastq file) data with minimap and miniasm. I was able to create the .paf.gz file with minimap which looks good. However when I’m trying to assemble with miniasm, I get an empty .gfa file. The command lines I am running are :

minimap/minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz #this one works and miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa #here reads.gfa is empty

Would you any idea what is the problem and how to solve it ?

Best regards,

Emma Corre

shehongbing commented 4 years ago

Hi, there,

Did you solve the problem, I had the same issue.