Trimming Fastq Reads for kallisto

[Paul_N_Hengen]

Does kallisto match reads that are below that of the K-mer length used to
create the index? For example, the default K-mer value for creating the index
for kallisto is N=31. If I set trimmomatic MINLEN=20 and I get some reads
trimmed to < 31 bases, are these tested against the hash of 31 bases within
the index and not found (inefficient, tested but not counted), ignored because
they are too small for the K-mer length (inefficient, tested for length and
ignored), or matched as a substring of the K-mer within the index and counted
(flexible, some amount of mismatch allowed)?