Input assemblies

Transcript assemblies used for evaluating Mikado, divided by subsection:- Input_assemblies_real_data.zip: assemblies derived from real data, see the "Performance of Mikado" section in the manuscript.- Input_assemblies_simulated_data.zip: assemblies derived from simulated data, see the "Performance of Mikado" section in the manuscript.- Input_assemblies_multiple_Isoform_Fraction.zip: StringTie and CLASS2 assemblies derived by varying the Minimum Isoform Fraction parameter. See the "Filtering lenient assemblies" section in the manuscript.- Input_assemblies_multiple_samples.zip: assemblies derived from real data using multiple samples RNA-Seq of A. thaliana; see the "Multi-sample transcript reconstruction" section in the manuscript.- Input_assemblies_pacbio.zip: alignments and assemblies of Illumina and PacBio reads; see the "Expansion to long read technologies" section in the manuscript.Except for the PacBio alignments, which are GMAP gff alignments, all assemblies are in GTF format and follow the pattern:-0---0.gtfE.g. the file:stringtie-0-tophat-err588042-0.gtfis a StringTie assembly derived from a TopHat2 alignment of sample ERR588042.Please see the manuscript and SnakeMake files in this repository for details on how these assemblies have been generated.