How to align a genome fasta file from NCBI to a reference genome?

Question

[ritafonsa]

Hi,

I want to align a genome published on NCBI (scaffold level) to a reference genome (chromosome level). I though bwa mem could work, but it is stuck, running for too long without any error message. Do you know any software that could do this? Also, I would like to call SNPs after the alignment.

Thanks!

[dthorbur]

I agree either mummer or minimap2 are good choices (don't know lastz). But as an aside, if the ploidy of the organism is anything but haploid you will lose a lot of variants that are lost when collapsing into a haploid reference sequence. It might be worth trying to find the original short or long read data they used to assembly the genome to call SNPs. They should be available in most bioproject accessions.

[Joe]

mummer is probably a better option for large pairwise alignments.

[GenoMax]

Please use a long read aligner like minimap2 or better still lastz (LINK) which is designed for chromosome sized pieces.

[vasudhapai]

hii can u pls tell me the file formats of the scaffold and chromosome level genomes please I'm also working on genome assemblies and I want to align a contig to a chromosome reference thanks

[dthorbur]

What's the purpose of aligning the contig to the chromosome reference? May change the tools that are suggested.

Answer 1

[Antonio R. Franco]

There is a version of a CUDA graphic accelerated version of lastz named SegAlign