Sequencing Requirements for Single Cell DNA

Specifications, Last Modified on June 29, 2018, Permalink

Single Cell DNA Libraries

Supported Sequencers: *

• Illumina® NextSeq 500/550 (High Output)
• Illumina® 2500 (Rapid Run)
• Illumina® 3000/4000
• Illumina® HiSeq X
• Illumina® NovaSeq

Recommended Sequencing Depth:

• 750,000 read pairs per cell (for human) enables accurate detection of 2 Mb events per single cell. Accurate detection of lower resolution events may be achieved at lower coverage. For more information on the impact of varying sequence coverage, please review the following page: Detailed Read Depth Guidance
• Only human and mouse have been tested.

Paired-end, single indexing: Single Cell DNA libaries are single-indexed. Although single indexing is recommended, if a dual-index configuration is used, use bcl2fastq’s --use-bases-mask or mkfastq’s --ignore-dual-index option to ignore the I2 read.

Read	Read 1	i7 Index	i5 Index	Read 2
Purpose	16bp 10x Barcode and gDNA	Sample Index	N/A	gDNA
Length **	100 or 150	8	0	100 or 150

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* Sequencing Performance Details

** Sample index reads must not be shorter than indicated. Any read can be longer than recommended. Additional bases in sample index reads must be trimmed using “cellranger-dna mkfastq” or Illumina’s “bcl2fastq“ prior to further analysis. Shorter read lengths will reduce the fraction of genome over which copy number is estimated