#+TITLE: RepeatExplorer documentation
#+HTML_HEAD_EXTRA: <link rel="stylesheet" type="text/css" href="style1.css" />
#+LANGUAGE: en
#+OPTIONS: html-postamble:nil

#+begin_export html 
<h1 id="clust"> Cluster annotation table </h1>
#+end_export

- Cluster :: cluster index, contain link to individual cluster report
- Supercluster :: Supercluster index, contains link inf individual supercluster report
- Proportion[%] :: Proportion of the reads in the cluster with respect to the amount of number of analyzed sequence.
- Proportions adjusted[%] ::  Adjusted genome proportion can differ from unadjusted value if the Perform automatic filtering of abundant satellite repeats was on. Sequences belonging to high abundance satellites were partially removed from all-to-all comparison and clustering. This causes that the Genome proportion estimate for these satellite is underestimated. Adjusted Genome proportion provide corrected estimate of ‘real’ genomic proportion for particular satellite repeat. 
- Number of reads ::  number of reads in the cluster
- Graph layout :: Preview of graph based visualization of sequence reads cluster. More detailed graph layout can be foun in individual cluster reports
- Similarity hits :: summarize the proportion of reads in the clusters with similarity to REXdb or DNA reference databases. Only hits with proportion above 0.1% are shown
- LTR detection  ::  Show if the LTR with primer binding site was detected on contig assembly and what type of tRNA is used for priming. 
- Satellite probability :: provide empirical probability that cluster represent satellite
- TAREAN classification  :: TAREAN divides clusters into five categories described in box 9.
- Consensus length :: For clusters analyzed by TAREAN module, the best estimate of monomer length is shown.
- Consensus :: The best consensus estimate reconstructed by TAREAN module
- Kmer analysis :: if cluster was analyzed by TAREAN, this field contains the link to the detailed TAREAN kmer analysis (box 10)
- Connected component index C,  Pair completeness index P, Kmer coverage :: statistics reported by TAREAN module
- |V|  :: Number of vertices of the graph
- |E|  :: Number of edges of the graph


#+begin_export html 
<h1 id="superclust"> Supercluster annotation table </h1>
#+end_export

 - Supercluster :: supercluster index
 - Reads :: number of reads in supercluster
 - Automatic classification :: Result of automatic supercluster classification
 - Similarity hits :: Number similarity hits against REXdb and DNA database are shown in the classification tree structure together with the number of reads assigned to putative satellite cluster  and information about detection of LTR/PBS. The parts of the tree without any evidences are pruned off.
 - TAREAN annotation :: Clusters which are part of supercluster and classified by TAREAN as putative satellite are listed here
 - Clusters :: hyperlinked list of clusters which are part of the superclusters. 

#+begin_export html 
<h1 id="tra"> Tandem repeat analysis </h1>
#+end_export

TAREAN divides clusters into five categories with corresponding files in the
archive:

    - High confidence satellites with consensus sequences in file ~TR_consensus_rank_1_.fasta~
    - Low confidence satellites with consensus sequences in file ~TR_consensus_rank_2_.fasta~
    - Putative LTR element with consensus sequences in file ~TR_consensus_rank_3_.fasta~
    - rDNA with consensus in ~TR_consensus_rank_4_.fasta~
    - other clusters – these clusters are not reconstructed by TAREAN because no potential tandem like structure was found.

Summary tables from TAREAN html report include following information:

    - Cluster :: cluster identifier
    - Proportion[%] ::  (Number of sequences in cluster/Number of sequences in clustering) x 100%
    - Proportion adjusted[%] ::
    - Number of reads :: Number of reads in the cluster
    - Satellite probability :: Empirical probability estimate that cluster sequences are derived from satellite repeat. This estimate is based on analysis of  manually anotated and experimentaly validated satellite repeats
    - Consensus length ::
    - Consensus :: Consensus sequence is outcome of kmer-based analysis and represents the most probable satellite monomer sequence, other alternative consensus sequences are included in individual cluster reports
    - Graph layout :: Graph-based visualization of similarities among sequence reads
    - Kmer analysis :: hyperlink to Individual clusters TAREAN kmer report (fig X, box 10)
    - Connected component index C :: Proportion of nodes of the graph which are part of the the largest strongly connected component
    - Pair completeness index P :: Proportion of reads with available mate-pair within the same cluster
    - Kmer coverage :: Sum of relative frequencies of all kmers used for consensus sequence reconstruction
    - |V| :: Number of vertices of the graph
    - |E| :: Number of edges of the graph
    - PBS score :: Primer binding site detection score
    - Similarity hits ::  similarity hits based on the search using blastn/blastx against built-in databases of known  sequences. By default, this will contain similarity hits to built in database which include rDNA sequences, plastid and mitochondrial sequences. If TAREAN was run within RepeatExplorer2 pipeline, it will also contain information about similarity hist against REXdb database. 

In individual clusters TAREAN report contain other variant of consensus
sequences sorted by kmer coverage score. For each consensus, corresponding
de-Bruijn graph representation and corresponding sequence logo is shown.

#+begin_export html 
<h1 id="kmer"> TAREAN k-mer analysis report </h1>
#+end_export

TAREAN module generates kmer analysis report for each cluster assigned to a putative satellite, rDNA or a putative LTR category. Monomer sequences  of putative tandem repeats  are reconstructed using k-mer based method using the most frequent k-mers. Several k-mer lengths are evaluated and the best estimated of monomer consensus sequence are reported. Kmer analysis summary contain the following information:
- k-mer length :: length of the k-mer used for monomer reconstruction
- Variant index :: Each kmer of given length can yield multiple consensus variant. Variants are indexed
- k-mer coverage score  :: is sum of proportions of all k-mer used for reconstruction of particular monomer. If the value is 1 then all kmers from corresponding cluster were used for reconstruction of monomer meaning that there is no variability. The more variable the monomer, the lower the k-mer coverage score.
- Consensus length :: length of estimated monomer
- Consensus :: consensus sequence shows the consensus sequence extracted from position probability matrix.
- k-mer bases graph :: the visualization of de-Bruijn graph. Each vertex corespond to single k-mer. Size of vertex is proportional to the kmer frequency. Path which was used to reconstruct monomer sequence is grey out.  
- Sequence logo  :: visualization of position probability matrices for corresponding consensus variant.