After filling the gaps, run_pbjelly output all the sequences in the file named 'jelly.out.fasta' under the file folder '2-results'.
Besides, for the detailed process information for each gap, you can refer the file 'gap_fill_status.txt' also under the file folder '2-results'.
We also generated a html report for run_pbjelly, which include contig N50 value, distribution of gap lengths, and et al. And the report files were placed under the file folder '3-reports' (comming soon). A simple statistics were generated under the file folder '3-reports', such as:
