Additional files for Lexa et al. HiC-TE publication

Additional files for Lexa et al. HiC-TE publication <strong>Additional file 1</strong> Suplementary Figure — Flow chart of the Nextflow HiC-TE pipeline (output from running Nextflow with the -graph switch) <strong>Additional file 2</strong> HiC-TE manual <strong>Additional file 3</strong> Suplementary Tables — HiC-TE Nextflow pipeline performance on a 4-core 3.0GHz Intel Ubuntu box and in the cloud (MetaCentrum metacentrum.cz). Numerical values are averages of 12 runs excluding TE-greedy-nester reference annotation (is needed only once) <strong>Additional file 4</strong> Suplementary Tables — Hi-C tomato (Solanum lycopersicum) leaf mesophyll sequencing runs from project SRP110225 (Dong et al., 2017) used to test the Nextflow pipeline. The individual runs represent different biological and technical replicates (see batch and plant numbers) <strong>Additional file 5</strong> PDF files with 6 complete sets of outputs, numbered by SRR ID and the name of output