Contig.

Question

[diegoestradamunoz]

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.

Answer 1

[GenoMax]

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.

[diegoestradamunoz]

Ah, ok thank you.