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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
419 stars 38 forks source link

minigraph and minimap2 alignment #73

Open 8banzhuan opened 2 years ago

8banzhuan commented 2 years ago

Hello，I use minigraph for read to rGFA alignment and i got a gaf size as 4479KB Then I used gfatools to convert the rGFA graph to linear FASTA and compared it with the same FASTQ file，Then I got a paf size as 8823KB，This happens because half of the reads are not aligned to rGFA relative to the linear reference sequence? Logically speaking, the graph structure should be better mapped, maybe my idea is wrong, I just involved in the field of bioinformatics Learning, thank you for your answer。 Good luck

Szhiha commented 1 year ago

Would you mind telling me how to generate a gaf file with contents? I have problems with it , because I use the command "minigraph -cx lr|sr graph.gfa query.fa > out.gaf" always generate an empty .gaf file, and I have tried several different test files.