Solexa and HiSeq

[dongshenglulv]

I'm very confused with the relationship of Solexa and HiSeq.
Is it true that HiSeq 2000 based on the technology of Solexa?

[lletourn]

Yes. They're both from illumina. Actually illumina bought solexa awhile back.

Solexa became GenomeAnalyzer. Then GenomeAnalyzer got a few upgrades (optics, flowcell layout, etc) until the GAIIx.

Then the hiseq came out. THe principals are the same, but they don't work the same way.

On the GA, the camera that takes pictures at given intervals, on the hiseq the camera does a linescan of the lanes of the flowcell.

The GA only reads the bottom of the flowcell, the hiseq reads top and bottom.

I won't list all the differences, you can go to illuminas site if you want more details.

[dongshenglulv]

Thank you so much

[deepika123]

hello..

if i say solexa reads then it is considered Hiseq2000 based technology or not. actually i have solexa sequencing data and i installed the Fastx tool for adopter removal but this tool is only for solexa and sanger reads so i did not understand that solexa reads including HTseq technology or not.

thanx in advance

[GenoMax]

hello..

if i say solexa reads then it is considered Hiseq2000 based technology or not. actually i have solexa sequencing data and i installed the Fastx tool for adopter removal but this tool is only for solexa and sanger reads so i did not understand that solexa reads including HTseq technology or not.

thanx in advance

Solexa was the name of the company that Illumina acquired back in 2006. Solexa pioneered the technology for sequencing that is still being used in principal with new Illumina sequencers.

Depending on the vintage of the data you are using there were multiple quality encoding formats (for fastq format). More information on that is here: http://en.wikipedia.org/wiki/FASTQ_format#Encoding

If you know that the data you have is using an older encoding method (i.e. "non-sanger" then you may have to pass right options to Fastx toolkit. If you are not sure what format your data is in (in terms of quality) then you can try the FastQC program: http://www.bioinformatics.babraham.a...ojects/fastqc/. It can generally identify the quality format and will display it in the general summary.

Trimmomatic is also a better option for trimming: http://www.usadellab.org/cms/?page=trimmomatic