minigraph - stable fa - shot sequences

[bioteksampath]

Hi @lh3,

I'm wondering why I'm encountering numerous short sequences in the stable fa (<100bp, >10,000 sequences). Additionally, I've noticed multiple headers in a single fa sequence.

Do you recommend any quality control steps after constructing the minigraph?
I used minigraph to generate an interactive GFA file for 50 genomes:

minigraph -cxggs 50_genoem_chr.fa  > 88_n99_chr_migraph.gfa
gfatools gfa2fa -s 88_n99_chr_migraph.gfa > 50lines_n99chr_migraph.stable.fa

sample stable.fa
`>Bna.1SN01.A01_49059_49213 >N1:33431 >N1:33605
TACAAACATGGCTGTGCATATGATATTATAATTGTTAGCTGGTATTCAATTGATTTTGTAAGTTATTATATACACCCCATACTCAAGACTCTTAAGAATTTGTTGTTGTTGTACGAGACTGTTAGCATGTTAAAGATTGACCCCAAAAAAAAAA

Bna.1SN01.A01_102616_102720 >N1:78908 >N1:78908
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT
Bna.1SN01.A01_118746_118749 >N1:102059 >N1:102112
TTC
Bna.1SN01.A01_137545_137553 >N1:112373 >N1:112643
ATATCTAC
Bna.1SN01.A01_189995_190021 >N1:159314 >N1:160100
GTATCTTTTATTTATTCCCCACATGC`

Thanks
sam