Additional file 2 of HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes

Additional file 2. Fig. S2: Outline of the AgRenSeq Snakemake workflow. Enriched Illumina reads are trimmed with fastp [18]. The k-mers present in these reads are counted with Jellyfish [19]. NLR Annotator is used to identify assembled contigs with signals of NLRs present [8], these contigs are then used to perform the association analysis [1]. The location of candidate contigs in a provided reference genome is assessed by BLAST [20].