NGS datasets

Introduciton

This deposity contains many kinds of sequencing datasets from Novogene. Any researchers, clinicians or collaborators who are interested in NGS can download freely. And we appriciate that you could give us any advice or suggestions.

1. Human Genome Sequencing

To compare with benchmark of GIAB, we provide genome sequencing data of HG002, which is one member of Ashkenazim son-father-mother trio, also named NA24385. The "High-confidence" variant calls are available for GRCh37 and GRCh38 under each genome at NCBI ftp or ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release.

• Whole Exome Sequencing

Kit for exome capture: Agilent SureSelect Human All Exon V6 Kit

Sequencing strategy: Illumina NovaSeq, PE150

sample source	left reads	right reads	md5sum	data size
HG002	HG002_novogene_wes_16g_rep1_R1.fq.gz	HG002_novogene_wes_16g_rep1_R2.fq.gz	md5	16G
HG002	HG002_novogene_wes_16g_rep2_R1.fq.gz	HG002_novogene_wes_16g_rep2_R2.fq.gz	md5	16G
HG002	HG002_novogene_wes_12g_R1.fq.gz	HG002_novogene_wes_12g_R2.fq.gz	md5	12G
HG002	HG002_novogene_wes_6g_R1.fq.gz	HG002_novogene_wes_6g_R2.fq.gz	md5	6G

• Whole Genome Sequencing

Sequencing strategy: Illumina NovaSeq, PE150

sample source	left reads	right reads	md5sum	data size
HG002	HG002_novogene_wgs_20g_R1.fq.gz	HG002_novogene_wgs_20g_R2.fq.gz	md5	20G
Novogene	Novogene_wgs_90g_R1.fq.gz	Novogene_wgs_90g_R2.fq.gz	md5	90G
Novogene	Novogene_wgs_120g_R1.fq.gz	Novogene_wgs_120g_R2.fq.gz	md5	120G
Novogene	Novogene_wgs_180g_l1_R1.fq.gz Novogene_wgs_180g_l2_R1.fq.gz	Novogene_wgs_180g_l1_R2.fq.gz Novogene_wgs_180g_l2_R2.fq.gz	md5	180G

2. Transcriptome Sequencing

Transcriptome or RNA sequencing can be ultilized to analysis many classes of RNA molecules, such as mRNA, non coding RNA, small RNA or RNAs from a single cell. To get a better view of data quality, we also sequence with ERCC spike-in control mixtures, which are used to evaluation gene expression measurement of new technique.

• mRNA Sequencing

species	left reads	right reads	md5sum	spike-in	data size
Human	Novogene_human_mrnaseq_rep1_R1.fq.gz	Novogene_human_mrnaseq_rep1_R2.fq.gz	md5	Y	15G
Human	Novogene_human_mrnaseq_rep2_R1.fq.gz	Novogene_human_mrnaseq_rep2_R2.fq.gz	md5	Y	15G
Human	Novogene_human_mrnaseq_rep3_R1.fq.gz	Novogene_human_mrnaseq_rep3_R2.fq.gz	md5	Y	15G
Arabidopsis	Novogene_arabidopsis_mrnaseq_rep1_R1.fq.gz	Novogene_arabidopsis_mrnaseq_rep1_R2.fq.gz	md5	Y	15G
Arabidopsis	Novogene_arabidopsis_mrnaseq_rep2_R1.fq.gz	Novogene_arabidopsis_mrnaseq_rep2_R2.fq.gz	md5	Y	15G
Arabidopsis	Novogene_arabidopsis_mrnaseq_rep3_R1.fq.gz	Novogene_arabidopsis_mrnaseq_rep3_R2.fq.gz	md5	Y	15G

• Whole RNA Sequencing

species	left reads	right reads	md5sum	spike-in	data size
Human	Novogene_human_wholernaseq_R1.fq.gz	Novogene_human_wholernaseq_R2.fq.gz	md5	N	15G

• Single Cell RNA Sequencing

species	left reads	right reads	md5sum	spike-in	data size
Arabidopsis	Novogene_arabidopsis_singlecell_R1.fq.gz	Novogene_arabidopsis_singlecell_R2.fq.gz	md5	N	7G

3. PacBio Sequencing

• Isoform Sequencing (Iso-Seq)

species	subread_bam	subread_bam_index	md5sum	data size
Human	Novogene_pacbio_isoseq_subreads.bam	Novogene_pacbio_isoseq_subreads.bam.pbi	md5

• Pacbio Genome Sequencing

species	subread_bam	subread_bam_index	md5sum	data size
Unknown	Novogene_pacbio_genome_subreads.bam	Novogene_pacbio_genome_subreads.bam.pbi	md5	20G

4. 10X Genomics

• 10X Single Cell Gene Expression

species	left reads	right reads	md5sum	data size
Human	Novogene_10x_singlecell_i1_R1.fq.gz Novogene_10x_singlecell_i2_R1.fq.gz Novogene_10x_singlecell_i3_R1.fq.gz Novogene_10x_singlecell_i4_R1.fq.gz	Novogene_10x_singlecell_i1_R2.fq.gz Novogene_10x_singlecell_i2_R2.fq.gz Novogene_10x_singlecell_i3_R2.fq.gz Novogene_10x_singlecell_i4_R2.fq.gz	md5	27G

• 10X Linked-Reads Genome Sequencing

species	left reads	right reads	md5sum	data size
Human	Novogene_10x_genome_i1_R1.fq.gz Novogene_10x_genome_i2_R1.fq.gz Novogene_10x_genome_i3_R1.fq.gz Novogene_10x_genome_i4_R1.fq.gz	Novogene_10x_genome_i1_R2.fq.gz Novogene_10x_genome_i2_R2.fq.gz Novogene_10x_genome_i3_R2.fq.gz Novogene_10x_genome_i4_R2.fq.gz	md5	100G

Citations

• GIAB - Genome in a Bottle
• ERCC - External RNA Controls Consortium

About Novogene (EN | CN)

Novogene is a leading provider of genomic services and solutions with cutting edge NGS and bioinformatics expertise and the largest sequencing capacity in the world. Novogene utilizes scientific excellence, a commitment to customer service and unsurpassed data quality to help our clients realize their research goals. The company has become a world-leader in NGS services, with 1,800 employees and multiple locations across the globe. Novogene’s depth of experience has resulted in the ownership of 49 NGS-related patents, as well as the publishing of over 1850 customer research papers, often in well-respected publications such as Nature and Science.