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.gtf

E.g. the file:

stringtie-0-tophat-err588042-0.gtf

is 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.