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Plant/Animal Whole Genome Sequencing

Whole genome re-sequencing, also known as WGS, enables the revealing of both common and rare mutations on the whole genome including Single Nucleotide Polymorphism (SNP), Insertion Deletion (InDel), Structure variation (SV), and Copy Number Variation (CNV). SVs make up a larger portion of the variation base than SNPs and have a greater impact on the genome, which has a significant effect on living organisms. Long-read resequencing allows for more precise identification of large fragments and complicated variations because long reads make it much easier to chromosomal crossing over complicated regions such as tandem repeats, GC/AT-rich regions, and hyper-variable regions.

Platform: Illumina, PacBio, Nanopore


Service Details

Demo Result

Featured Publication

1.Service Advantages

Extensive experience in genome sequencing for over 1000 species.

Over 800 published cases with an accumulative impact factor of over 4000.

Comprehensive bioinformatics analysis on variation calling and function analysis.

2. Service Specifications

Platform

Library

Recommended seq depth

Illumina

PE 150

For SNP, InDel calling ≥ 10x

For SV, CNY calling ≥ 30x

 

 

Nanopore

 

8 kb

For SV, CNY calling ≥ 20x 

Pacbio

CCS

15 kb

For SNP, InDel, SV, CNY calling ≥ 10x

3. Sample Requirements

Platform

Conc.(ng/μL)

 

Amount (ng)

 

Purity

 

Agarose gel

 

OD260/280

OD260/230

1. Clear main band with no or limited degradation observed on gel.

2. No or limited RNA or protein contamination

 

Illumina

≥1

≥30

 

-

-

Nanopore

 

≥30

Depends on data yield

10μg/cell

1.7-2.2

≥1.5

Pacbio

CCS

≥50

1.7-2.2

1.8-2.5

4. Bioinformation Analysis

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5. Service Work Flow

sample delivery

Sample delivery

Pilot experiment

DNA extraction

Library Preparation

Library construction

Sequencing

Sequencing

Data analysis

Data analysis

数据上传-03

Data delivery


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  • 1) Statistics of Genome Mapping

    Table 1 Statistics of mapping result

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    Figure 1 Distribution of insert size and reads coverage.

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    2) Variate Detection

    Figure 2 Statistics and annotation of SNP/INDEL/SV among Samples

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    Figure 3 Genome-wide distribution of vatiations

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    3) Functional annotation of variations 

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    2019

    Nature communications

    Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement

    2020

    PNAS

    The evolutionary origin and domestication history of goldfish (Carassius auratus)

    2021

    Plant Biotechnology Journal

    Reference genomes of the two cultivated jute species

    2021

    Plant Biotechnology Journal

    Genomic signatures of vegetable and oilseed allopolyploid Brassicajuncea and genetic loci controlling the accumulation of glucosinolates

    2019

    Molecular Plant

    Whole-genome resequencing of a world-wide collection of rapeseed accessions reveals genetic basis of their ecotype divergence

    2022

    Horticulture Research

    Genome-wide association analysis provides molecular insights into the natural variation of watermelon seed size

    2021

    Journal of Experimental Botany

    Genome-wide association study identifies variants of GhSAD1 conferring cold tolerance in cotton

    2021

    Journal of Experimental Botany

    Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed

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