Chunk size, kmers or seqs?

[mr-eyes]

Rethinking regarding the chunk size, should we define the chunk size as the number of sequences or the number of kmers?

Chunk size as the number of sequences should work when the sequence lengths are relatively small. In genomes for example, if we set the chunk size to 10k that will consume a lot of memory per single chunk. On the other hand, it will work smoothly when processing transcripts due to their short and the average length is small.

Chunk size as the number of kmers will work just fine on the previous examples and we can set a fixed multiplier of thousands or millions.

@drtamermansour what do you think?

[mr-eyes]

Error Duplicate #12