This post is related to, but different (a continuation) from my earlier post at ABySS run problems seeking help with running the genome assembler software - ABySS. I got my ABySS runs going.
But in order to assess the optimal k-mer, I was trying values 21-97 (increments of 2).
Related to this attempt, at k-mer value>64 (i.e. 65), the STDERR log terminated with the line - "ABYSS: ../Common/Kmer.h:48: static void Kmer::setLength(unsigned int): Assertion `length <= 64' failed."
Obviously my university's compute cluster has ABySS compiled and configured to allow k-mers <= 64.
Some context for my questions below - I have 2*150 PE Illumina HiSeq400 reads from fungal spore DNA (haploid genome). Read length trimming has resulted in size distribution between 41 (min) and 150 (max).
1a. How do I execute ABySS with k-mer value > 64, but WITHOUT re-compiling? Is that possible? I ask in the context of what is written at https://insidedna.me/tool_page_assets/pdf_manual/abyss.pdf, which reads:
"The default maximum k-mer size is 64 and may be decreased to reduce memory usage or increased at compile time. This value must be a multiple of 32 (i.e. 32, 64, 96, 128, etc):"
1b. If running k-mer > 64 is NOT possible without recompiling, is there a work-around that allows re-setting local variable(s) on just my compute cluster account?
Is there a theoretical / practical limit on k-mer value > default 64? I know SPAdes, for example, permits as high as 127. What is it for ABySS? Is it 128?
Is checking k-mer value > 64 necessary? Which is a different question from whether it is possible?