I have been trying all the different exome enrichment kits available during the last years.
I am now wondering what the real performance of the new Nextera Rapid Exome enrichment kit (37 or 62 Mb target) is compared to the competitors.
I used a lot of the TrueSeq exome enrichment which was a good deal considering quality and costs compared to Nimblegen and Agilent.
Now that the TrueSeq libraries are only available until the end of 2013 and the TrueSeq exome enrichment have been eliminated, the only choice is between Agilent or Nextera.
Nimblegen does not have an optimized protocol for the enrichment of Nextera libraries so when the TrueSeq library prep kit will be over, there will be nothing to enrich with the Nimblegen kits.
Agilent is not my favourite for many reasons (high quantity requested in input or high # of PCR Cycles requested, high costs, low % of reads on target when a few samples are pooled prior to enrichment etc.).
Can someone tell me what's the % of reads on target with the Nextera libraries and exome enrichment? Did you compare it to previous exomes using other kits?
With the other kits I could expect 65-80% of reads on target depending on the condition and kit used.
What real coverage do you get on avarage pooling n ( ... you name it) Nextera samples per lane?
With Illumina TrueSeq libraries and Enrichment I used to get a 35-45X coverage from a pool of 6 samples per lane (2x100bp) (62 Mb target).
Thank you in advance for sharing your experience.
I am now wondering what the real performance of the new Nextera Rapid Exome enrichment kit (37 or 62 Mb target) is compared to the competitors.
I used a lot of the TrueSeq exome enrichment which was a good deal considering quality and costs compared to Nimblegen and Agilent.
Now that the TrueSeq libraries are only available until the end of 2013 and the TrueSeq exome enrichment have been eliminated, the only choice is between Agilent or Nextera.
Nimblegen does not have an optimized protocol for the enrichment of Nextera libraries so when the TrueSeq library prep kit will be over, there will be nothing to enrich with the Nimblegen kits.
Agilent is not my favourite for many reasons (high quantity requested in input or high # of PCR Cycles requested, high costs, low % of reads on target when a few samples are pooled prior to enrichment etc.).
Can someone tell me what's the % of reads on target with the Nextera libraries and exome enrichment? Did you compare it to previous exomes using other kits?
With the other kits I could expect 65-80% of reads on target depending on the condition and kit used.
What real coverage do you get on avarage pooling n ( ... you name it) Nextera samples per lane?
With Illumina TrueSeq libraries and Enrichment I used to get a 35-45X coverage from a pool of 6 samples per lane (2x100bp) (62 Mb target).
Thank you in advance for sharing your experience.
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