Computational protocol: Prospecting for viral natural enemies of the fire ant Solenopsis invicta in Argentina

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Protocol publication

[…] Sequences were aligned to the Solenopsis invicta reference genome downloaded from http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEAQ01#contigs using the Burrows-Wheeler Aligner (bwa-0.7.5a), a software package for mapping low-divergent sequences against a large reference genome []. The S. invicta unmapped reads were selected and converted to FASTA format using NextGENe-2.3.4 (SoftGenetics, State College, PA). Each read was then filtered and retained if the median score was ≥ 20 and base number ≥ 25. Unmapped and filtered individual MiSeq sequences were analyzed using BLASTX [] against the curated Swiss Protein database (http://www.uniProt.org; download date 11/14/2014). Sequences returning an expectation score less than 10−5 were tabulated.Based on the BLASTX results, each sequence was annotated and assorted taxonomically. The sequences were binned into the following groups: Animal, Plant, Fungi, Bacteria, Archaea, Phage, and Non-phage virus. Also at this stage, sequences exhibiting identity to Enterobacteria phage phiX174, an internal control for Illumina processing [] were removed and not considered in subsequent analyses. […]

Pipeline specifications

Software tools BWA, NextGENe, BLASTX
Application WGS analysis
Organisms Solenopsis invicta, Human poliovirus 1 Mahoney, Euphaea formosa, Solenopsis invicta virus 1, Viruses