Current version: 1.0 (March 2022)
-- Read our article in Applications in Plant Sciences (Open Access)
by Wu Huang, Royal Botanic Garden Edinburgh
SSSNPs
- Python 3+
- R
Required for BWA version of the pipeline and for the intron and depth calculation scripts:
- samtools 1.2 or later (Read/Write BAM files to save space).
NOTE:
Full instructions on running the pipeline, including the requred formats of the files, a step-by-step tutorial using a small test dataset, is available on our wiki: link
You will also need to construct a "target" file of gene regions. The target file should contain one gene region per sequence, with exons "concatenated" into a contiguous sequence. For more information on constructing the target file, see the wiki, or view the example file in: test_dataset/test_targets.fasta
There can be more than one "source sequence" for each gene in the target file. This can be useful if the target enrichment baits were designed from multiple sources-- for example a transcriptome in the focal taxon and a distantly related reference genome.