ena-STUDY-LMU-28-05-2018-13:37:09:179-855
Development and improvement of an Antarctic fur seal (Arctocephalus gazella) genome assembly
The aim of this project was to use PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly. First, the program GapCloser v1.12 was used to fill gaps in the original assembly (Humble et al. 2016, https://datadryad.org//resource/doi:10.5061/dryad.8kn8c.2) based on the paired-end information of the original Illumina reads. Following this, SMRT (Single Molecule Real Time) sequencing data from the DNA used for the original genome assembly (NCBI SRA: BioSample SAMN04159679) was generated. Next, PBJelly v15.8.24 and blasr (https://github.com/PacificBiosciences/blasr) were used with default parameters to align the PacBio sequencing reads to the gap-closed assembly to generate a hybrid genome. Then, a two-step strategy was used to remove any indels introduced by SMART sequencing technology. First, Quiver (contained in SMRT/2.3.0 suite; GenomicConsensus v0.9.2) was used with the refineDinucleotideRepeats option to perform initial assembly error correction. Next, the original illumina reads (from PRJNA298406) were mapped to the Quiver generated assembly used BWA MEM v0.7.15. Finally, PILON (v1.22) was used to perform error correction to generate an improved assembly (v1.4 and deposited in this BioProject). The genome assembly consists of 6169 scaffolds (N50:6.2MB) such that 50% of the final assembly is contained within the longest 108 scaffolds.
The aim of this project was to use PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly. First, the program GapCloser v1.12 was used to fill gaps in the original assembly (Humble et al. 2016, https://datadryad.org//resource/doi:10.5061/dryad.8kn8c.2) based on the paired-end information of the original Illumina reads. Following this, SMRT (Single Molecule Real Time) sequencing data from the DNA used for the original genome assembly (NCBI SRA: BioSample SAMN04159679) was generated. Next, PBJelly v15.8.24 and blasr (https://github.com/PacificBiosciences/blasr) were used with default parameters to align the PacBio sequencing reads to the gap-closed assembly to generate a hybrid genome. Then, a two-step strategy was used to remove any indels introduced by SMART sequencing technology. First, Quiver (contained in SMRT/2.3.0 suite; GenomicConsensus v0.9.2) was used with the refineDinucleotideRepeats option to perform initial assembly error correction. Next, the original illumina reads (from PRJNA298406) were mapped to the Quiver generated assembly used BWA MEM v0.7.15. Finally, PILON (v1.22) was used to perform error correction to generate an improved assembly (v1.4 and deposited in this BioProject). The genome assembly consists of 6169 scaffolds (N50:6.2MB) such that 50% of the final assembly is contained within the longest 108 scaffolds.