Table 4.

Sources of and Solutions to Potential Errors ^a

Problem	Possible cause	Solution
ntEdit does not make any edits and/or Sealer does not fix any regions	The supplied k values may be too low or high	Sweep a larger range of k values. For ntEdit, check the _changes.tsv output files to determine which k values produce the most edits. For Sealer, check .sealer_log.txt file to determine which k values close the most gaps. Adjust the parameter values accordingly.
Sealer step takes too long	The provided k value is too low	The realistic lower‐bound for k is 40. Run the protocol again with higher k values.
Assembly accuracy metrics from BUSCO or QUAST deteriorate	False positive rate of ABySS‐Bloom Bloom filter may be too high.	Increase the Bloom filter size (b parameter) or try larger k values
The ntEdit+Sealer Makefile gives the error “No rule to make target…”	Parameter values or files were passed or named incorrectly	Ensure input files are named correctly and that parameters are passed as expected. Run ntedit‐sealer help or check the ntEdit+Sealer Github page for more details.

^a Potential problems that a user may encounter when running ntEdit+Sealer protocol and corresponding potential causes and solutions.