# RepeatExplorer documentation

# Cluster annotation table

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

# Supercluster annotation table

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.

# Tandem repeat analysis

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.

# TAREAN k-mer analysis report

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.