Hi,
we are working with a GaXll Sequencer from Illumina and screening for SNP's. I read some publications about external Basecaller and thought about their useability.
There are many external base calling tools which can outperform the Illumina's default Basecaller (bustard). A nice overview are shown here:
The results of Ibis and naiveBayesCall looks good.
Also a nice discussion is here:
But there are error-correction tools like ECHO (http://www.ncbi.nlm.nih.gov/pmc/arti...0/?tool=pubmed)
This improvement of quality values could be helpful for SNP-calling.
How did you thinking about the usage of external Basecaller or is the usage of error-correction tools more profitable?
we are working with a GaXll Sequencer from Illumina and screening for SNP's. I read some publications about external Basecaller and thought about their useability.
There are many external base calling tools which can outperform the Illumina's default Basecaller (bustard). A nice overview are shown here:
The results of Ibis and naiveBayesCall looks good.
Also a nice discussion is here:
But there are error-correction tools like ECHO (http://www.ncbi.nlm.nih.gov/pmc/arti...0/?tool=pubmed)
This improvement of quality values could be helpful for SNP-calling.
How did you thinking about the usage of external Basecaller or is the usage of error-correction tools more profitable?