Resequencing Mycobacteria with Miseq

[docsascha]

Dear All,

We are doing resequencing of various bacteria, but it seems to be complicated to do Mycobacteria sequencing, regardless if its M. tuberculosis or non tuberculous Mycobacteria.

DNA Extraction was done after cooking the samples for 10 Minutes using either Qiagen or MagnaPure Compact.
For the Library preparation and sequencing nextera Kits were used.

Results were awful, just a few reads

Maybe some of you can give us some advice

THX
Alexander

[nucacidhunter]

The species genome has high GC content but it is less likely cause. It could be due to library itself or sequencing issues. It would be helpful to post library trace and more info on sequencing system. Was XT kit used for library prep or Nextera DNA?

[soleulloa]

Hi docsascha!
Did you tried a new run?? Tell us the results! I'm interested in mycobacterium sequencing in my lab
Regards

[pmiguel]

Somebody had us sequence a mycobacterium strain. Just did a normal Illumina No-PCR TruSeq library construction and did 10% of a HiSeq lane. ABySS-PE assembly had N50 of 208kb.

--
Phillip

[JakobHedegaard]

Hi,
We have just completed sequencing of several isolates of Mycobacterium abscessus using Nextera XT library prep (on a Janus NGS Express robot) and sequencing (NextSeq 500). Fine data...
Docsascha, please add some details if you still need some comments.
Cheers,
/Jakob