Papers Updated November 4, 2020

References

AODP

AODP is used to run barcode reference building and sample analysis in Virtool. It was integrated into Virtool through a joint project with its Developer, Wen Chen.

Zahariev M, Chen W, Visagie CM & Lévesque CA. 2018. Cluster oligonucleotide signatures for rapid identification by sequencing. BMC Bioinformatics: 19. doi: 10.1186/s12859-018-2363-3.

Bowtie2

Bowtie2 is used to map reads to known viral and subtraction genomes.

Langmead B & Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods: 9. doi: 10.1038/nmeth.1923.

FLASH

FLASH is used to join overlapping paired-end reads during barcode analysis using AODP.

Magoč T & Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics: 27. doi: 10.1093/bioinformatics/btr507.

HMMER

HMMER is used to predict viral protein motifs in the NuVs novel virus discovery workflow.

Eddy SR. 2011. Fast gapped-read alignment with Bowtie 2. PLoS Comput Biol: 7. doi: 10.1371/journal.pcbi.1002195.

Pathoscope

A modified version of the Pathoscope2 strain identification framework is used to detect known viruses.

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA & Johnson WE. 2014. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome: 2. doi: 10.1186/2049-2618-2-33.

Skewer

Skewer is used to trim sample reads.

Jiang H, Lei R, Ding S-W & Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics: 15. doi: 10.1186/1471-2105-15-182.

SPAdes

SPAdes is used to assemble contigs in the NuVs novel virus discovery workflow.

Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VW, 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. doi: 10.1089/cmb.2012.0021.

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