DOI: 10.57760/sciencedb.29212
title: A data African swine fever virus collected from Domestic pigs in Nigeria
title: A data African swine fever virus collected from Domestic pigs in Nigeria

description: 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 &lt; 20X for ONT data and NGS &gt; 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 
description: 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 &lt; 20X for ONT data and NGS &gt; 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