Two short questions about haploclique capabilities ?

cbg-ethz / haploclique

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

GNU General Public License v3.0

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Two short questions about haploclique capabilities ? #43

Closed jblamyatifremer closed 6 years ago

jblamyatifremer commented 7 years ago

Dear Haploclique Creators,

1- Could we use Haploclique on DNA virus dataset ? 2- Does Haploclique could manage large insertion elements (>1000 bp) ? It could be problematic since the read length is samller compare to deletion length indeed this information is not contain in Bam file (I see the help page that structural variant is not fully supported).

Cheers,

MaryamZaheri commented 7 years ago

Hi,

1- Sure, you can use it on DNA virus datasets. 2- Haploclique can handle large structural variation. However, we are improving the performance of the basic algorithm and later this will be re-activated.