How to know the positions of contigs in a reference genome

Question

[Ashi]

Hi I am quite new to Bioinformatics and this site has always helped me. I have generated contigs (FASTA file) of E coli from short read assemblers like PaKman, Minia. I want to know the positions of these contigs in the reference genome now. Is there any tool to do that? I have seen the earlier posts here saying that blast can give the positions but I could not get the command line to do so. I know quast gives you the position of the misaligned contig positions but I want to know the positions of the all the contigs that I have got from the short read assembler.

Thanks for all the help.

Answer 1

[GenoMax]

You can simply align the contigs to E. coli genome. minimap2 or lastz would be good options.

Answer 2

[Jordi]

Another option that works well for aligning FASTA files is MAFFT (https://mafft.cbrc.jp/alignment/software/).