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Inconsistency between assembly_graph.gfa and assembly.fasta

Open MrTomRod opened this issue 1 year ago • 4 comments

Dear Mikhail

contig_3 in assembly_graph.gfa is missing in assembly.fasta:

$ grep ">" assembly.fasta 
>contig_1
>contig_2

Preview of assembly_graph.gfa:

H       VN:Z:1.0
S       edge_1  TATTTTATGAAAGAGGTGATTTTTATGCCGAAAAGA... (54kb)	dp:i:1494
S       edge_2  TCACTTATTTTCCATTCTCTTTTCATAAGATCTCTG... (3.4mb)	dp:i:451
S       edge_3  ACAAATATAATTTCATTTAAAACCTTGTCACAAAAT... (25kb)	dp:i:34
L       edge_1  +       edge_1  +       0M      RC:i:1243
L       edge_2  +       edge_2  +       0M      RC:i:343
L       edge_3  +       edge_3  +       0M      RC:i:0
P       contig_2        edge_2+ *
P       contig_1        edge_1+ *
P       contig_3        edge_3+ *

Visualization using gfaviz --no-gui --render --group-labels --output assembly_graph.gfa.svg assembly_graph.gfa:

assembly_graph gfa

Is that a bug?

MrTomRod avatar Jan 19 '24 14:01 MrTomRod