Sequencing Requirements for De Novo Assembly

Specifications, Last Modified on January 12, 2018, Permalink

Supported Sequencers

• Illumina HiSeq X Ten/Five
• Illumina HiSeq 2500 Rapid Run Mode
• Illumina HiSeq 4000 Standard Usable, but observed to produce contigs half as long as those from HiSeq X, for 38x human data.

Preliminary

• Illumina NovaSeq Standard (Preliminary results look comparable to HiSeq X results)

Not Tested

• Illumina HiSeq 2500 High output
• Illumina MiSeq Standard Performance likely comparable to HiSeq 2500 in rapid run mode.

Not Recommended

• Illumina NextSeq Standard

Sequencing Requirements

Read	Read1	i7 Index	i5 Index	Read2
Purpose	10x Barcode + nmer + Genome Sequence	Sample Index	Not used	Genome Sequence
Length	150	8	0	150

Read length: Supernova requires as input 2x150 base reads. Use of significantly shorter or longer reads may result in inferior assemblies. Supernova does not accept reads that are less than 125 base pairs.

Read1 contains the 10x Barcode (16 bp) + nmer (6 bp) + Genome Sequence (128 bp)

Sequencing Depth

38x-56x. Higher coverage within this range will generally give better results. Coverage higher than 56x may not improve results, and could make them worse. For highly polymorphic organisms, we recommend 56x.

Achieving Success with De Novo Assembly