Comparing Genomic Assemblies To Find Indels

Question

[K. Wyatt Mcmahon]

Hello everyone,

We've sequenced a YAC containing a stretch of human DNA as an insert. We know what the insert sequence is supposed to be. However - as you could imagine - Illumina-based sequencing has found a number of differences from what we though the sequence should be. We've gone through and identified the insertions and deletions manually (as well as SNPs). But, we would like to simply compare the consensus sequence from the Illumina assembly with the proposed sequence, and get a table of insertions, deletions, and SNPs.

Can anyone help us do this? Surely there is a program which easily aligns long sequences and outputs a list of mismatches and indels!

Thanks in advance,

Wyatt

Answer 1

[Vitis]

I think MUMmer is the standard application for this. However, it's not quite trivial to create the consensus from your short reads, you may choose de novo assembly or reference-based methods.