Hi!

I have ~163000 contigs (a single FASTA file) and I want to map them to a refernce genome (also a FASTA file). Is there any way to do it? I have tried bowtie2, but could not work out its nuances.

Any help appreciated!

Thanks
Bowtie2 is a short read mapper and, although it can be used to map long sequences, it probably won't be good at it, specially if the query and reference are even moderately divergent.

In addition to the suggestions by https://www.biostars.org/u/33094/ and https://www.biostars.org/u/18713/ , there is also [LAST][1]. 

Another option to consider is [QUAST][2], an assembly evaluation tool. Quast uses minimap2 to align one (or more) query genomes to a reference genome, and in addition to the alignment, it will provide a number of metrics comparing the query to the reference. 

  [1]: http://last.cbrc.jp/
  [2]: http://quast.sourceforge.net/quast