#+TITLE: RepeatExplorer based Assembly Annotation Pipeline

* Tools in repository
**  Extract Repeat Library from RepeatExplorer Archive
(=extract_re_contigs.xml=)

This toll  will extract library of repeats  based on RepeatExplorer2 analysis. Library is available as fasta file.

** Format repeat library
(=format_repeat_library.xml=)

This tool append classification of repeats to library of repeats. Type of repeat is then part of sequence name in format:

~>sequence_id#classification_level1/classification_level2/...~ this enable to specify classification hierarchy
Classification of sequneces in library is provided using  =CLUSTER_TABLE.csv= (part of RE2 output)

This file can then be used for annotation of repeat in your assembly:
** Repeat Annotation
(=repeat_annotate_custom.xml=)

 Internally annotation is performed using RepeatMasker search. Output from RepeatMasker is parsed to remove duplicated and overlaping annotations, Conflicts in annotations are resolved using hierarchical classification of repeats provided in custom database

* test data

- ~test_assembly_1.fasta~ with ~test_db_1_satellites.fasta~ (include CLASS followed by double underscore - syntax 1)
- ~test_assembly_2.fasta~ with ~test_db_2_RE_repeats.fasta~ (include full hierarchical classification)



#+begin_comment
create tarball for toolshed:
tar -czvf ../repeat_annotation_pipeline.tar.gz --exclude test_data --exclude .git  .

#+end_comment>