I've got contigs from de novo (Spades) assembly (approx 175 contigs of length 200 bp to 11 kb), and want to map these to a reference sequence and make a new consensus. I have tried using Bowtie2 and I do get an output. However, all the aligned contigs have been truncated down to 60 bp.
I've tried changing the Bowtie2 index to "large index", Bowtie2 is run using the -f and -U options.
Any help appreciated.