Bacterial reference-guided assembly vs. de-novo assembly unicycler?

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  • idba

    • I de-novo assembled the short reads with unicycler and produced a phylogenetic tree with all 35 genomes. I am planning to use https://github.com/loneknightpy/idba to re-assemble the short reads using their corresponding most closely related "perfect" genome as a reference.

  • RagTag

    Tools for fast and flexible genome assembly scaffolding and improvement

    • Has anyone used ragtag to correct bacterial assemblies (https://github.com/malonge/RagTag/wiki/correct) ? Is it helpful?

  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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