Ah, ok thank you.
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diegoestradamunoz •
Contig.
Hello, i got this contig after an assembling with megahit:
>k127_133265 flag=1 multi=5.0000 len=2169
GTGCTCTTCCGATCTTGAAATTGTTCCA..
Do you know what means flag=1 and multi=5.0000?
Thank you.
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diegoestradamunoz •
1 answer
Explained by the developers here: https://github.com/voutcn/megahit/issues/54
flag is a tag to represent the connectivity of a contig in the assembly graph. flag=1 means the contig is standalone, flag=2 a looped path and flag=0 for other contigs.
multi is roughly the average kmer coverage. But the figure is not precise and if you want to quantify the coverage of a contig, I would suggest you align the reads back to the contigs by short read aligners.
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