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1. Screening BIGSI for SGI1 REs

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maxlcummins edited this page Nov 12, 2019 · 1 revision

High-throughput SGI1-related element screening with BIGSI

BIGSI was used in combination with a custom Snakemake workflow to allow high-throughput screening of a snapshot of SRA (Prior to December 2016). The custom Snakefile can be found here. This workflow results in the generation of a CSV file containing Sequence-read archive accession numbers of genomic datasets containing one or more of elements of the backbone of SGI1 as well as species identification based on Kraken and Bracken analysis.

For information on using Snakemake, please see the Snakemake documentation here.

References:

  • Bradley, P., Den Bakker, H., Rocha, E., McVean, G. and Iqbal, Z., 2017. Real-time search of all bacterial and viral genomic data. BioRxiv, p.234955.
  • Köster, J. and Rahmann, S., 2012. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics, 28(19), pp.2520-2522.
  • Wood, D.E. and Salzberg, S.L., 2014. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome biology, 15(3), p.R46.
  • Lu, J., Breitwieser, F.P., Thielen, P. and Salzberg, S.L., 2017. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science, 3, p.e104.
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