I have several CPU nodes connected to the same network mounted directory. I want to parallelize the abyss-map step after abyss generates unitigs.

When I run abyss-map on my reads, it outputs a message saying it is generating a suffix array for the mapping. Does it store that on disk? Or does it just store it in memory for the mapping?

If I parallel run several abyss-map in the same directory, will the suffix array generated overwrite the suffix array generated by other abyss-map runs?
Hi Damian,

`abyss-map` builds the indexes in memory by default, so there should be no conflict about running multiple instances on the same file in parallel.

However, you can also use `abyss-index` to pre-build the indexes (.fai and .fm files). Any subsequent `abyss-map` runs will re-use those index files (similar to how it works with BWA), which allows you to run `abyss-map` more quickly and with a smaller memory requirement. (The initial indexing step requires an amount of RAM that is about 10 times the size of the input FASTA file.)