{"id":765,"date":"2021-11-09T11:57:30","date_gmt":"2021-11-09T10:57:30","guid":{"rendered":"https:\/\/wp.unil.ch\/gtf\/?page_id=765"},"modified":"2026-03-19T21:37:48","modified_gmt":"2026-03-19T20:37:48","slug":"illumina-sequencers","status":"publish","type":"page","link":"https:\/\/wp.unil.ch\/gtf\/illumina-sequencers\/","title":{"rendered":"Short Reads Sequencers"},"content":{"rendered":"\n

3 Short Reads sequencers are currently operated by GTF: NovaSeq<\/span> <\/a>and MiSeq<\/span><\/a> from Illumina, and Aviti <\/a>from Element Biosciences<\/p>\n\n\n\n

Sequencing prices are available on our LIMS<\/a><\/p>\n\n\n\n

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NovaSeq<\/span> 6000<\/span><\/strong><\/p>\n\n\n\n

This is one of the latest sequencer from Illumina. It offers high output for a very competitive price for large flow cells (S4, and to a lesser extent S2).<\/p>\n\n\n\n

4 types of flow cells with different outputs are available.
All flow cells are patterned and ideally require libraries with Unique Dua<\/strong><\/a>l Indexing<\/strong><\/a>.<\/p>\n\n\n\n

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Flow cells can be used for 100 cycles, 200 cycles, or 300 cycles sequencing runs
These cycles can be split and used either for single end (SR or SE) or paired end runs (PE)
Please discuss actual limitations with GTF staff<\/span><\/em><\/p>\n\n\n\n

Standard settings proposed by GTF are SR 100 cycles<\/strong> \/ PE 150 cycles<\/strong> \/ PE 28+90 cycles<\/strong> (10X single cell settings).
The entire flow cell (2 or 4 lanes) must be processed with the same cycling conditions. Requests not matching these standard settings may therefore wait longer (to fill the flow cell) before being processed.<\/p>\n\n\n\n

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NovaSeq specifications<\/a><\/p>\n<\/div><\/div>\n\n\n\n

WARNING<\/span><\/span>: Data generated on the NovaSeq may not directly compare to legacy HiSeq data
\u2022<\/strong> NovaSeq is a 2-colors system while HiSeq were 4 colors<\/span>
\u2022<\/strong> Novaseq goups Q-scores into 4 bins while HiSeq used > 70 Q-scores (see details<\/a>)<\/span>
\u21a0 This change is mostly neutral for gene expression analysis (e.g. RNAseq, bulk or single cell)
\u21a0 It may have a non negligible impact on variant analysis
\u21a0 Analysis pipeline codes may require updating<\/p>\n\n\n\n

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Aviti<\/strong><\/p>\n\n\n\n

Element Biosciences sequencer Aviti is an alternative to Illumina sequencing for moderate throughput short read projects.<\/p>\n\n\n\n

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Aviti specifications<\/a><\/p>\n<\/div><\/div>\n\n\n\n

Its main characteristics are:<\/p>\n\n\n\n