Hi there,
in my GFA output file I'm seeing what appear to be duplicates of the same scaffold represented by different segments:
P NODE_1_length_144681_cov_2.716323_1 8012+ *
P NODE_1_length_144681_cov_2.716323_2 7322+ *
P NODE_1_length_144681_cov_2.716323_3 1502+ *
P NODE_1_length_144681_cov_2.716323_4 8010- *
P NODE_1_length_144681_cov_2.716323_5 7714- *
P NODE_1_length_144681_cov_2.716323_6 8046+ *
P NODE_1_length_144681_cov_2.716323_7 8058+ *
P NODE_1_length_144681_cov_2.716323_8 7320+ *
P NODE_1_length_144681_cov_2.716323_9 8060+ *
P NODE_1_length_144681_cov_2.716323_10 7570+,7766-,8066-,7766+,7964+ *
P NODE_1_length_144681_cov_2.716323_11 7920+ *
P NODE_1_length_144681_cov_2.716323_12 7866- *
P NODE_1_length_144681_cov_2.716323_13 7626+ *
P NODE_1_length_144681_cov_2.716323_14 8038- *
P NODE_1_length_144681_cov_2.716323_15 8032- *
P NODE_1_length_144681_cov_2.716323_16 8044+ *
P NODE_1_length_144681_cov_2.716323_17 8036+ *
P NODE_1_length_144681_cov_2.716323_18 7988+ *
P NODE_1_length_144681_cov_2.716323_19 7982- *
P NODE_1_length_144681_cov_2.716323_20 7970+ *
P NODE_1_length_144681_cov_2.716323_21 2070+ *
P NODE_2_length_3833_cov_1.524087_1 8000- *
P NODE_2_length_3833_cov_1.524087_2 7998+ *
P NODE_3_length_2275_cov_1.414414_1 7882+ *
P NODE_3_length_2275_cov_1.414414_2 8062- *
P NODE_3_length_2275_cov_1.414414_3 7974- *
P NODE_3_length_2275_cov_1.414414_4 7170- *
P NODE_4_length_983_cov_1.275862_1 7524+ *
P NODE_4_length_983_cov_1.275862_2 7904- *
P NODE_5_length_431_cov_0.757979_1 7744+ *
P NODE_6_length_356_cov_0.993355_1 8008+ *
Could you explain why these different segments are being collapsed into the same nodes? Is there some sequence identity threshold where segments are collapsed into single nodes for the purpose of the scaffolds.fasta file but not for the purpose of the .GFA assembly graph?
Thank you!
Hi there,
in my GFA output file I'm seeing what appear to be duplicates of the same scaffold represented by different segments:
Could you explain why these different segments are being collapsed into the same nodes? Is there some sequence identity threshold where segments are collapsed into single nodes for the purpose of the scaffolds.fasta file but not for the purpose of the .GFA assembly graph?
Thank you!