Mapping soft for de novo assembly

Question

[takoyaki]

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 !

Thanks

Answer 1

[GenoMax]

I think de novo assembled multi fasta file is different from complete whole genome fasta file.

It is different only in the sense that it is not perhaps complete as a model genome reference you would download from NCBI/Ensembl. Otherwise it is just a multi-fasta file and you can create indexes from it to use as a reference with any aligner you want. Depending on how well your assembly worked you would want to make sure that you remove redundancy that may be present in the contigs.