I am hoping to use CAMSA to merge two sets of scaffolds produced by different algorithms. Upon upload, NCBI requires information about what evidence was used to join contigs around gaps. NCBI allows this information in an annotation .tbl file with assembly gaps:
100 201 assembly_gap
gap_type within scaffold
linkage_evidence align-genus
420 521 assembly_gap
gap_type within scaffold
linkage_evidence paired-ends
Since there are possibly complex cases where contigs are joined in the CAMSA assembly (using either scaffolded input or both), is it possible to extract this information automatically from the output for the final CAMSA sequences?
I am hoping to use CAMSA to merge two sets of scaffolds produced by different algorithms. Upon upload, NCBI requires information about what evidence was used to join contigs around gaps. NCBI allows this information in an annotation .tbl file with assembly gaps:
Since there are possibly complex cases where contigs are joined in the CAMSA assembly (using either scaffolded input or both), is it possible to extract this information automatically from the output for the final CAMSA sequences?
Thanks for the help!