WSSV-IN-LS.fasta

The genome sequences of two White Spot Syndrome Virus (WSSV) strains from India (WSSV-IN-LS and WSSV-IN-NS) that were previously studied by Sivakumar et al 2018 could not be found in public databases. The raw Illumina read sequences corresponding to these WSSV strains were downloaded from the NCBI Short Read Archive (SRR3233836 - WSSV-IN-LS and SRR3233837 - WSSV-IN-NS) and adapter sequences and low-quality bases (including poly-G and low complexity sequences) were removed using fastp v0.20.0 (Chen et al 2018). For each sample, sequences were normalised using BBNorm, part of BBTools v38.03 (Bushnell) (parameters used: ecc=t, bits=16, prefilter) prior to de novo assembly with SPAdes v3.13.1 (Bankevich et al 2012) using the only-assembler flag and k-mers of 21, 33, 55, 77, 99 and 127. Assembled contigs were blasted against a reference WSSV genome sequence (WSSV-CN, GenBank Accession AF332093.3) using Blastn v2.9.0+ (Camacho et al 2009) to identify contigs representing WSSV.<br><br>This file contains the contigs that represent the WSSV-IN-LS genome sequences.<br><b>References</b>Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.Bushnell B. https://sourceforge.net/projects/bbmap/.Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421.Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890.Sivakumar, S., Vimal, S., Abdul Majeed, S., Santhosh Kumar, S., Taju, G., Madan, N., Rajkumar, T., Thamizhvanan, S., Shamsudheen, K.V., Scaria, V., Sivasubbu, S., and Sahul Hameed, A.S. 2018. A new strain of white spot syndrome virus affecting Litopenaeus vannamei in Indian shrimp farms. J Fish Dis. 41:1129–1146.