A data African swine fever virus collected from Domestic pigs in Nigeria

Data DescriptionThis dataset comprises genomic sequences from five Nigerian domestic pig samples screened for African swine fever virus (ASFV). Four samples were sequenced using both Illumina short-read (NGS; 2×150 bp) and Oxford Nanopore Technologies (ONT) long-read platforms, while one sample was sequenced exclusively with ONT. Data Generation & Processing - Library Preparation:  - Illumina libraries prepared with NEBNext UltraExpress™ DNA Library Prep Kit (NEB #E3325S/L) and sequenced with NovaSeq 6000.  - ONT libraries sequenced on PromethION platform with Ligation sequencing gDNA - NativeBarcoding Kit 96 V14 (SQK-NBD114.96). - Hybrid Assembly (4 samples):  - Raw Illumina FASTQ and ONT FASTQ files were co-assembled using SPAdes v3.14.1 with hybrid mode, followed by polishing with Racon v1.5.0, Medaka and Pilon v1.24. - ONT-Only Assembly (1 sample):  - ONT reads were assembled with Flye v2.9.1 and polished using Racon v1.5.0 + Medaka. File Contents1. Raw Data:   - FASTQ.gz: Illumina (NGS)   - FASTQ.tar.gz: ONT raw reads.   - Metadata: the metadata are found bellow in the list of samples names. 2. Assembled Data:   - FASTA: Final ASFV genomes (hybrid SPAdes assemblies for 4 samples; Flye assembly for 1 sample).   - Contig statistics (N50, genome completeness) are reported bellow in the list of samples names. Quality Notes - Missing Data: read depth of < 20X for ONT data and NGS > 45X.  - Contigs were manually reviewed via BLAST against the ASFV reference. Reuse & Compatibility - Open formats (FASTQ, FASTA) compatible with tools like FastQC, and Minimap2. LIST OF SAMPLES NAMES1. Nigeria-LA74 fastq A33_DKDL240036295-1A_22Y2CLLT3_L6_1.fq.gz A33_DKDL240036295-1A_22Y2CLLT3_L6_2.fq.gz OxfordNanopore_native 95_fastq_pass.tar.gz Domestic pig African swine fever virus 2. Nigeria-VPD805 fastq A51_DKDL240036297-1A_22KVVKLT4_L8_1.fq.gz A51_DKDL240036297-1A_22KVVKLT4_L8_2.fq.gz OxfordNanopore_native 93_fastq_pass.tar.gz Domestic pig African swine fever virus   3. Nigeria-DDS922 OxfordNanopore_native 92_fastq_pass.tar.gz 7 Domestic pig African swine fever virus  4. Nigeria-DDS943 fastq A613_DKDL240036300-1A_22KVVKLT4_L8_1.fq.gz A613_DKDL240036300-1A_22KVVKLT4_L8_2.fq.gz  OxfordNanopore_native 91_fastq_pass.tar.gz Domestic pig African swine fever virus  5. Nigeria-613 fastq A65_DKDL240036299-1A_22KVVKLT4_L8_1.fq.gz A65_DKDL240036299-1A_22KVVKLT4_L8_2.fq.gz OxfordNanopore_native 90_fastq_pass.tar.gz Domestic pig African swine fever virus