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Is there a bug in HybridScaffold?

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  • Is there a bug in HybridScaffold?

    When i finished the running of HybridScaffold, some sequences will duplicate two or three times in file of the EXP_REFINEFINAL1_bppAdjust_cmap_Gl_contigs_fasta_N GScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta.


    [daojuny@m8int02 agp_fasta]$ grep '^>tig00002147' EXP_REFINEFINAL1_bppAdjust_cmap_Gl_contigs_fasta_N GScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

    >tig00002147 len=11459595 reads=16123 covStat=3353.30 gappedBases=no class=contig suggestRepeat=no suggestCircular=no_subseq_11263614:11275583_obj

    >tig00002147 len=11459595 reads=16123 covStat=3353.30 gappedBases=no class=contig suggestRepeat=no suggestCircular=no_subseq_11383879:11459595_obj

    [daojuny@m8int02 agp_fasta]$ grep '^>tig00000022' EXP_REFINEFINAL1_bppAdjust_cmap_Gl_contigs_fasta_N GScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta

    >tig00000022 len=16249439 reads=21141 covStat=5980.96 gappedBases=no class=contig suggestRepeat=no suggestCircular=no_subseq_7259257:7262484_obj

    >tig00000022 len=16249439 reads=21141 covStat=5980.96 gappedBases=no class=contig suggestRepeat=no suggestCircular=no_subseq_16147389:16148513_obj

    >tig00000022 len=16249439 reads=21141 covStat=5980.96 gappedBases=no class=contig suggestRepeat=no suggestCircular=no_subseq_7928097:7944583_obj

  • #2
    I know the reason that some conflict contigs were cutted at the conflict site, but it only added tag at the end of sequence name!

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