Introduction

De novo assembly is used to piece together shorter sequenced fragments (reads) into more extensive continuous segments (contigs and scaffolds), which are often required for subsequent analyses. This is a key step in many analyses where a reference genome is unavailable.

Workflow

An overview of our de novo assembly pipeline is shown below. Key steps include sequence quality evaluation using FastQC, read trimming and filtering using Trimmomatic, and de novo assembly using SPAdes.

The final results of the pipeline are outlined in blue.

1. An HTML formatted sequencing quality report produced by FastQC.
2. A FASTA formatted file containing assembled contigs produced by SPAdes.
3. A FASTA formatted file containing assembled scaffolds produced by SPAdes.
4. A final analysis report in PDF format containing a description of the methods used and some additional QC and summary figures.

Pricing

Our current price for this analysis is $60 per sample.

References

Please refer to these resources and tools that form an integral part of the pipeline process.

1. FastQC – A quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
2. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170
3. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102

Contact

Please contact us for a free consultation. We look forward to working with you on your analysis projects.

Phone: 509-368-6668

Email: Spok.GenomicsCore@wsu.edu

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