Egyptian Water Buffalo
First Full Genome Sequencing and Annotation
Animals used in Sequencing

Main Objectives

This sequencing initiative provides a draft genome sequence of the Egyptian water buffalo (Bubalus bubalis) to the scientific community.

Water Buffalo (Bubalus bubalis)

Water buffalo (Bubalus bubalis) is an important source of meat and milk in countries with relatively warm weather. Compared to the cattle genome, a little is done to reveal the genome structure of the buffalo. Production of a high resolution draft for whole genome of Egyptian buffalo (Bubalus bubalis) will increase the role of genome in the different disciplines of livestock research and promote agricultural sustainability for Egypt.


We introduce a high quality draft assembly of the Egyptian buffalo genome, as a representative of the water buffalo species. The sequencing was based on the Next Generation Sequencing technology. The assembly was achieved using a reference-based assembly workflow, which dramatically reduces the computational complexity of the assembly process and integrates different public resources to improve the assembly quality.

Identification of genetic features

Identification of genetic features within the sequenced genomes, such as genes, repeats, etc, which enable better understanding of the animal traits, physiology, domestication and evolution of the buffalo species. We also introduce further analysis, including genome annotation, variations among different animals from the same species, and comparison to the mammalian genomes.


Genome is sequenced using 5500xl SOLiD sequencer


The sequencing was based on the 5500xl SOLiD sequencer, which is a next generation sequencing technology. We achieved about 50-60x coverage of the genome, to enable good sequencing results. We used different types of libraries to produce two sets of reads

Single-ended Reads

Single-read sequencing involves sequencing DNA from only one end, and is the simplest way to utilize Solid sequencing, it is a cheaper than paired-end method

Mate-paired Reads

Each one of the pairs is 60 bps long and the two pairs are separated with certain distance in the genome. We used so far 2 sets, one set where the distance is 1000 bps and another set where the distance is 3000 bps.


  • Mapping Reads

    The workflow is based on using a reference genome, which is the cattle in our case, to sequence the target genome. The use of the reference genome is intended to speed up the assembly process without comprising the quality of the assembly.

  • Contig Assembly

    To capture the contiguous parts of the Buffalo genome, The algorithm works by combining reads mapped to the reference genome and de-novo assembly to create the contigs from the reads.

  • Repeat Analysis

    To spot repetitive parts of the genome and categroize them into different repeat families.

  • Scaffolding

    The scaffolding process runs in a multistep manner using mate-paired reads along with evidences coming from the reference genome to reduce the complexity of the scaffolding problem.

  • Genomic Annotation

    Genome annotation of the assembled genome involves the determination of genes with their exon-intron structure.

  • Comparative Genomics

    Comparison to genomes of other species and identifying rearrangement events

Egyptian Water Buffalo Genome Data

Download full water buffalo genome data

Egyptian Water Buffalo Genome From Nile University

Here download contig and scaffolds and links to NGS sequencing data

Egyptian Water Buffalo Genome From NCBI

Here download contig and scaffolds and links to NGS sequencing data

Our Team

Egyptian Water Buffalo Genome Consortium

A group of scientists from Agricultural Genetic Engineering Research Institute (AGERI) and Nile University.



The Center and the research project is funded by the Science and Technology Development Fund (STDF), Egypt.


NGS Data Analysis

Bioinformatics Workflow

Our analysis pipeline is optimized to speed up the analysis. It also combines information from public resources to improve the assembly. We used a number of tools including velvet, Bowtie, SHRiMP, BLAST, BLAT in a complex pipeline to finish the assembly and annotation. Go the Tavaxy Workflow