Skip to main content
Fig. 1 | Genome Medicine

Fig. 1

From: INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance

Fig. 1

INSaFLU bioinformatics workflow. The diagram (see schematic legend) illustrates all steps of the bioinformatics pipeline developed and implemented in the INSaFLU web platform, enrolling six core modules: (1) read quality analysis and improvement, (2) type and sub-type identification, (3) variant detection and consensus generation, (4) coverage analysis, (5) alignment/phylogeny, and (6) intra-host minor variant detection. Among other features, INSaFLU also determines “putative mixed infections” at two levels: (i) if more than one type, HA or NA subtype or lineage is detected and/or (ii) if the relative proportion of intra-host SNVs at frequency 1–50% (minor iSNVs) and 50–90% satisfies empirically derived criteria (specific alerts are also generated for each case). A detailed description of the INSaFLU outputs is presented in Table 1. Documentation for each module, including software settings and current versions, is provided at the website (https://insaflu.insa.pt)

Back to article page