Programs and documentation accompanying the paper: K. Weitemier, S.C.K. Straub, R. Cronn, M. Fishbein, A. McDonnell, R. Schmickl, and A. Liston. 2014. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics Applications in Plant Sciences 2(9): 1400042.
A protocol for developing probes for targeted sequence capture from an input of genomic and transcriptomic data is contained within Data Supplement S1: Building_exon_probes.sh. This file is both a program that can be run in a Linux environment, and a helpful document with detailed notes.
A workflow for analyzing the raw reads obtained from the Hyb-Seq protocol is described in Data Supplement S2.
assembled_exons_to_fastas, blat_block_analyzer, and grab_singleton_clusters are all companion programs integrated into either the probe development or read analysis pipelines.
Example datasets have been added: genome.fasta and transcriptome.fasta.
NOTE: The latest version of CD-HIT (4.6.1) contains a bug that appears when using the example data provided here. To successfully use the example data one should either use a CD-HIT version prior to 4.6 or use the patched version supplied here.
Copyright (c) 2014 K. Weitemier, S.C.K. Straub, R. Cronn, M. Fishbein, A. McDonnell, R. Schmickl, and A. Liston