Some users have reported that normalize-by-median.py will utilize more memory than it was configured for. This is being investigated in #266
If your k-mer table is truncated on write, an error may not be reported; this is being tracked in #443. However, khmer will now (correctly) fail when trying to read a truncated file (See #333).
Paired-end reads from Casava 1.8 currently require renaming for use in normalize-by-median and abund-filter when used in paired mode. The integration of a fix for this is being tracked in #23
Some scripts only output FASTA even if given a FASTQ file. This issue is being tracked in #46