Question: aligning to circular sequence
gravatar for yaximik
9 weeks ago by
yaximik0 wrote:

In regard to 7 yrs old discussion about aligning linear to circular sequences - is anyone aware of aligners that can handle such alignment properly? For alignment purposes, for example, CLC-Bio Genomic Workbench does not seem to be aware if sequence is circular, although it can show rCRS mtDNA as circular. Yet it cannot properly align to it a linear sequence that is should align between pos. 16022-origin-1280 to circular rCRS. Nor can Geneious, for another example.

alignment • 246 views
ADD COMMENTlink modified 6 weeks ago by 6mrsbrun0 • written 9 weeks ago by yaximik0

Since both of those are commercial programs have you contacted their respective tech supports about this?

ADD REPLYlink written 9 weeks ago by genomax59k

Yes, I guess they are scratching pumpkins... I just wanted to know if anyone in the community is aware of other possibilities, like open source...

ADD REPLYlink written 9 weeks ago by yaximik0

Is it NGS data ? Because i did it on times on NGS data with bwa and to make this possible i just merge 2 references together ....

ADD REPLYlink written 9 weeks ago by Titus770

No, this is just alignment of a contig previously assembled separately. CLC Bio developers confirmed that their Genomics Workbench aligner cannot handle circularity. As workaround they suggested either to use their Map to a Reference tool, which can handle circularity, or to align to a duplicated circular sequence.

ADD REPLYlink written 9 weeks ago by yaximik0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

BTW, have you looked at this: Aligning Circular Sequences (old thread but has ideas/tools).

ADD REPLYlink written 9 weeks ago by genomax59k

Have you considered Circlator?

ADD REPLYlink written 9 weeks ago by dylan.lawrence10
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