NLGenomeSweeper

NLGenomeSweeper is a command line bash pipeline that searches a genome for NBS-LRR (NLR) disease resistance genes based on the presence of the NB-ARC domain using the consensus sequence of the Pfam HMM profile (PF00931) and class specific consensus sequences built from Vitis vinifera. This pipeline can be used with a custom NB-ARC HMM consensus protein sequence(s) built for a species of interest or related species for greater power, separately for each type of NBS-LRR (TNLs, CNLs, NLs) and combine them into a single fasta file for use. This pipeline shows high specificity for complete genes and structurally complete pseudogenes. However, candidate regions are identified but may not necessarily represent functional genes and does not itself do gene prediction. A domain identification step is also included and the output in gff3 format can be used for manual annotation of NLR genes. Therefore, it is primarily for the identification of NLR genes for a genome where either no annotation exists or a large number of genes are expected to be absent due to repeat masking and difficulties in annotation. For many genomes this may be the case. (2019-08-26)