Question: Looking for a genome /draft genome aligner with the these features
0
gravatar for novice
3.1 years ago by
novice830
United States
novice830 wrote:

I have assembled a draft genome of s. pombe that I would like to compare to the reference. My purpose is to study structural variations (rearrangements, insertions/deletions, etc.) between the two genomes. Mauve is a good tool that has been serving my purpose thus far, but it turns out that it doesn't detect duplications, i.e. if a sequence from the reference is found twice in the draft genome; it only aligns it to one of them, and the other is labelled as not mapped. 

The features that I'm looking for in in an aligner are the following:
1. Detecting duplications and labelling them.
2. Good detailed output, including for example non-mapped contigs, contigs with multiple alignments, contigs with break-points (contigs that have a part mapped to one region and another part mapped to a different region.)
3. Quality, publication-fit figures.
4. Moves contigs to where they mapped in the reference (like Mauve contig mover).
 

I hope that there exits a software that does all of that.

Thank you.

mauve alignment assembly • 967 views
ADD COMMENTlink written 3.1 years ago by novice830
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1533 users visited in the last hour