search

Unaimend / bionim

A collection of useful algorithms and data structures for bioinformatics
12 stars 2 forks source link

FastQ parsing #3

Open andreas-wilm opened 3 years ago

andreas-wilm commented 3 years ago

Hello, not really an issue, just some information regarding FastQ/Fasta parsing

FastQ parsing in Nim is implemented here https://github.com/andreas-wilm/nimreadfq, which uses Heng Li's superfast kseq. There are two slower alternatives (the above contains a benchmark):

  1. Heng Li implemented Nim native FastQ parsing called FastX Reader (see https://github.com/lh3/klib.nim/blob/master/klib.nim)
  2. Then there is Jonathan Badger's Nimbioseq https://github.com/jhbadger/nimbioseq which also contains a FastQ parser. Note that this contains a number of other useful methods, you might want to consider including.
Unaimend commented 3 years ago

Thank you very much, I will have a look and nimreadfq, and nimbioseq. I of course like that version von Heng Li's library is quite a lot faster then the alternative. But maybe on could work on improving the speed of Jonathan's package, not sure how feasible that is.