Arabidopsis thaliana gene set reconstructed with EvidentialGene

METHODS
Component over-assembly gene sets from
de-novo assemblies of 3 RNA-seq sources,
without use of chromosomes, or other species genes
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evg3arath
  RNA source project http://www.ncbi.nlm.nih.gov/bioproject/PRJNA323955
  At cultivar:col-0 ; Illumina HiSeq 2000 paired end sequencing, root and other tissues
  From Virginia Tech, Song Li; 2016-11-18,
  doi: 10.1016/j.devcel.2016.10.012
  5,102,350 gene assemblies were generated from this RNA sample with 11 assembly runs.
  These were classified/reduced to 37,393 locus transcripts, plus 128,412 alternates 
  with Evigene methods.
  
evg4arath
  RNA source project http://www.ncbi.nlm.nih.gov/bioproject/PRJNA316113
    At cultivar:Col-0; Illumina HiSeq 2500, from Univ. CAMBRIDGE
  RNA source project http://www.ncbi.nlm.nih.gov/bioproject/PRJNA336053
    At cultivar:Col-0; Illumina HiSeq 2000, paired end sequencing, from 
  5,039,388  gene assemblies were generated from these two RNA samples with 10 assembly runs.
  These were classified/reduced to 36,347 locus transcripts, plus 135,007 alternates 
  with Evigene methods.

evg5arath
  The two Evigene gene sets, evg3 from a single source for strict comparison
  of methods, and evg4 adding 2 other RNA sources for more complete genes,
  are merged into a public set evg5, using transcript-only classification.
  This produced a set of 34,299 locus transcripts, plus 132,604 alternates. 
  
  This set is further classified by mapping to AtTAIR10 chromosomes,
  including reassignment of locus transcripts among alternates and paralogs,
  and removal of redundant same-locus extra transcripts.  Alternates were
  validated with RNA-seq mapped introns, and those lacking unique
  alternate spliced exon/intron chains were removed.
  
Genes assembled 2017-Jan/Feb, by D.G. Gilbert, gilbert at indiana edu
EvidentialGene methods for producing and reducing RNA over-assemblies are outlined
at http://eugenes.org/EvidentialGene/about/
RNA assemblers for Illumina paired short reads:
  velvet/oases:  velvet1.2.10, oases_0.2.08, 2013
  soap-trans:    SOAPdenovo-Trans v1.03, 2013
  idba_tran:     idba-1.1.1, 2013, https://code.google.com/p/hku-idba/ 
  trinity:       trinity/v2.4.0, 2017.02
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pacbio16arath
  Pac-Bio RNA data and assembly, using PacBio software/methods 
  RNA source project http://www.ncbi.nlm.nih.gov/bioproject/PRJNA306427
  From Virginia Tech, Song Li; 2016-11-18,
  same author, tissue, RNA source as used for Illumina, PRJNA323955
  doi: 10.1016/j.devcel.2016.10.012
  
RNA genes are extracted and assembled from 12 raw SRA PacBio RNA data entries (hdf5 files,
e.g. http://sra-download.ncbi.nlm.nih.gov/srapub_files/SRR3655756_SRR3655756_hdf5.tgz),
with Pacific Biosciences SMRTAnalysis software, ConsensusTools.sh and pbtranscript.py, 
of smrtanalysis_2.3.0.140936.  This was obtained from Pac. Bio., installed and run
as per directions. 

Only the RNA source data of project PRJNA306427 is used in this assembly,
although external data sets such as a chromosome assembly can be added to further
improve genes (in the nature of Cufflinks, StringTie or other assemblers 
that merge RNA short reads with chromosomes).
  
These Pac-Bio gene assemblies are not used  in evg3arath or 4 gene sets,
in order to compare results. However they can be used as input transcripts,
mixed with others, as part of the over-assembly that EvidentialGene methods
reduce to an accurate, non-redundant gene set. 
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Chromosome assemblies used
  At TAIR10, cultivar:Col-0, NCBI genomes GCF_000001735.3_TAIR10,	PRJNA116
  At Ler 2016, cultivar:Ler, NCBI genomes GCA_001651475.1, PRJNA311266
  
Reference gene sets:
  At Araport11 gene set, 2016 release, built on At TAIR10 chromosomes
  Theobroma cacao, Thecc7, 2017 Evigene set update, eugenes.org/EvidentialGene/plants/cacao/
  Citrus clementina, from NCBI Genomes, GCF_000493195.1_Citrus_clementina_v1.0

Alternate At gene model set for comparison
  AUGUSTUS models built on At Ler 2016 chromosome assembly, 
  obtained from NCBI genome annotation, GCA_001651475.1, PRJNA311266
  
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