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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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assembly.gfa contains more contigs than assembly.fasta #603

Closed mwittchen closed 1 year ago

mwittchen commented 1 year ago

Hello, I am assembling ONT R10 LSK114 Reads of cultivated bacteria with flye (2.9-b1768). When I'm inspecting the assembly.gfa in Bandage, there is one more (short) contig than in the assembly.fasta. Shouldn't the number of contigs be identical in assembly.gfa and assembly.fasta as they are both the final output?

Best Manuel

mikolmogorov commented 1 year ago

Hi Manuel,

One contig may contain multiple graph unitigs, this is why the number of sequences in assembly.fasta is often smaller.