##
## dfamseq 3.x
##

Overview
--------
Dfamseq is Dfam's collection of reference genomes and benchmark 
sequences.  Each assembly consists of a genomic reference file 
(dfamseq) and a GARLIC generated artificial genome (benchmark) 
modeled on the assembly.

Structure ( essential files )
-----------------------------
  ../dfamseq/<assembly_id>/
      README                  : Details on how the data was obtained
      README.source           : Details provided by the sequencing center
      <*>.gz                  : A FASTA file containing the original assembly
      genome.trf.bed          : TRF mask of genome (dfamseq) using <= 12mers
      dfamseq                 : Concatentation of all sequences for 
                                assembly ( ids begin with 1)
      dfamseq.trf.bed         : TRF annotations (typ <= 5mer) for dfamseq
      sequence.names          : Sequence IDs 
      dfamseq.mask            : TRF masked assembly
      dfamseq.mask.ssi        : sfetch index
      dfamseq.mask.2bit       : A two bit version of the dfamseq file
                  
      benchmark               : GARLIC benchmark
      benchmark.mask          : TRF masked benchmark
      benchmark.mask.ssi      : sfetch index
      assembly.dat            : JSON file containing the data stored in
                                   dfam.assembly table.