BioMicroCenter:Singular Sequencing: Difference between revisions

Revision as of 13:47, 28 May 2025

Singular Sequencing

The Center currently hosts a G4 platform by Singular Genomics. Singular’s G4 platform is a short-read mid-throughput sequencing platform delivering adequate sequencing data through its proprietary sequencing-by-synthesis chemistry at a significantly competitive price point.

Service	Singular Sequencing	Minimum reads per lane are guaranteed if: the BMC has performed quality control, the samples are high-complexity, especially for the first 10 nt of read 1, and submitted libraries are at least 2 nM. Workflow Library prep options for DNA or RNA are available for Singular sequencing. Singular library fragment size is verified via AATI's Fragment Analyzer. Singular library is quantified via qPCR. Requirements All 4 bases (A, G, C, T) must appear within the first 10 cycles of read 1. Lane-by-lane requests must be 50 or 150 paired-end and compatible with TruSeq, Nextera, TruSeq, smRNA and Solexa sequencing primers. All other requests will require a 4 lane minimum since all lanes use the flowcell's sequencing primers and this includes Illumina libraries which have been converted. For standard lane-by-lane requests, the first index will be read off the S1 region of the final library, and index 2 will be read off the S2 region. Compared to a typical Illumina library, a Singular index 1 would be the reverse compliment of the i5 index, whereas index 2 would be the reverse compliment of the i7 index.
INPUT	Singular libraries
MIN VOLUME	12 uL
MIN CONCENTRATION	4 nM
INCLUDED SERVICES	Quality Control:Fragment Analyzer and qPCR Singular Sequencing Demultiplexing
ADDITIONAL SERVICES	Quality Control Singular library preparation
DATA FORMATS	FASTQ (stored 1 year)
QUALITY CONTROL	FASTQC Basic run metrics (alignment rate, complexity) Basic RNAseq metrics (where applicable) Basic paired end metrics (where applicable) Contamination checks
PRICING	LINK
SUBMISSION	MIT - ilabs

The G4 Platform

SPEC	G4
SEQUENCER
READS/LANE Low number is minimum per lane for standard libraries	F3 per Lane: 50-100 M
RUN TIME	50 PE 11 hours 150 PE 24 hours
KITS AVAILABLE	100nt 300nt
KNOWN APPLICATIONS	RNAseq including single cell Gene Expression Exome Target Enrichment Metagenomics
KEY NOTES	4-color chemistry Patterned flow cell 4-lanes per flow cell 4-flow cells per run Index replacement or anchor expansion of Illumina libraries
THANKS TO	Singular Genomics

@@ Line 4: / Line 4: @@
    !width=100| Service
    !width=250| Singular Sequencing
+!'''Minimum reads per lane are guaranteed if:
+*the BMC has performed quality control,
+*the samples are high-complexity, especially for the first 10 nt of read 1, and
+*submitted libraries are at least 2 nM.'''
+=== Workflow ===
+Library prep options for [https://openwetware.org/wiki/BioMicroCenter:DNA_LIB DNA] or [https://openwetware.org/wiki/BioMicroCenter:RNA_LIB RNA] are available for Singular sequencing. <br> Singular library fragment size is verified via [https://openwetware.org/wiki/BioMicroCenter:QC AATI's Fragment Analyzer]. <br> Singular library is quantified via qPCR.
+===Requirements===
+<OL>
+<LI>All 4 bases (A, G, C, T) must appear within the first 10 cycles of read 1.
+<LI>Lane-by-lane requests must be 50 or 150 paired-end and compatible with TruSeq, Nextera, TruSeq, smRNA and Solexa sequencing primers.  All other requests will require a 4 lane minimum since all lanes use the flowcell's sequencing primers and this includes Illumina libraries which have been converted.
+<LI>For standard lane-by-lane requests, the first index will be read off the S1 region of the final library, and index 2 will be read off the S2 region.  Compared to a typical Illumina library, a Singular index 1 would be the reverse compliment of the i5 index, whereas index 2 would be the reverse compliment of the i7 index.
    |-
    |INPUT || Singular libraries