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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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No sequences in gfa - unable to convert to fasta #45

Closed lpryszcz closed 6 years ago

lpryszcz commented 6 years ago

Hi, how do you convert .gfa to .fasta? I've found a few posts recommending awk one-liner, but there are no sequences in .gfa. 

awk '/^S/{print ">"$2"\n"$3}' run.gfa | head
>utg000001l
*
>utg000002l
*
>utg000003l
*
>utg000004l
*
>utg000005l
*
lh3 commented 6 years ago

Use miniasm -f reads.fq overlap.paf