Repeated paths in GFA

[cjprybol]

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!

[asl]

There is no way to represent paths with gaps (= scaffolds) in GFA 1.0 format. Therefore, each scaffold is represented by multiple of contiguous paths in the assembly graph. See https://cab.spbu.ru/files/release3.15.2/manual.html#spadesoutsec for more examples.