how to get a sequence from read fragments with ref sequence?

Question

[Aaron]

Hello my friends, I currently get some read fragments and a reference genome sequence. How can I get the whole sequence from these read fragments and the reference genome sequence? I trid minimap2. It seems it can generate only mapping info. I also looked at minimap. Howevery, it seems it only support denovo assembly, without using the reference sequence. So dear my friends, do you know how to get the whole sequence from read fragments and reference sequence? Is there any pipline or tools to suggest? Thanks very much.

[WouterDeCoster]

the whole sequence from read fragments and reference sequence

It is unclear what you mean with that.

[Aaron]

Thanks for your reply. Actually, I got many read fragments, which belong to a genome sequence. These fragments are read from parts of this sequence, and maby have overlaps. Also the reference genome is given. Can I use these infomation to restore the original sequence from these fragments? Thank you.

[Pierre Lindenbaum]

extract the variants as a VCF file and then invoke FastaAlternateReferenceMaker ? https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker

[Aaron]

Thank you. Let me try.