I am now de novo sequence analysis and now finished de novo assemble and got multi fasta file. I want to make sam file by running mapping software after de novo assembly.
There are several software of mapping, like bowtie2, bwa, hisat2, STAR, tophat2.
I think de novo assembled multi fasta file is different from complete whole genome fasta file. Are they able to mapping even if it is not reference sequence but de novo assembled multi fasta file ? Which supports de novo assembled result ?
Also, if there is recommendation, please tell me !