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Inconsistency between assembly_graph.gfa and assembly.fasta
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
:
Is that a bug?