Mercurial > repos > petr-novak > repeat_annotation_pipeline2

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author petr-novak
date Tue, 12 Oct 2021 07:43:54 +0000
parents cf3cea0a3039
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2:3f8ae272f4f3 3:e955b40ad3a4
2 2
3 * Tools in repository 3 * Tools in repository
4 ** Extract Repeat Library from RepeatExplorer Archive 4 ** Extract Repeat Library from RepeatExplorer Archive
5 (=extract_re_contigs.xml=) 5 (=extract_re_contigs.xml=)
6 6
7 This toll will extract library of repeats based on RepeatExplorer2 analysis. Library is available as fasta file. 7 This toll will extract library of repeats based on RepeatExplorer2 analysis. Library is available as fasta file. Tool also filter out all the contig parts which has read depth and length below threshold. Parts of contigs with read depth below threshold are hardmasker. Contigs with full hardmasking are removed completelly
8 8
9 ** Format repeat library 9 ** Format repeat library
10 (=format_repeat_library.xml=) 10 (=format_repeat_library.xml=)
11 11
12 This tool append classification of repeats to library of repeats. Type of repeat is then part of sequence name in format: 12 This tool append classification of repeats to library of repeats. Type of repeat is then part of sequence name in format:
16 16
17 This file can then be used for annotation of repeat in your assembly: 17 This file can then be used for annotation of repeat in your assembly:
18 ** Repeat Annotation 18 ** Repeat Annotation
19 (=repeat_annotate_custom.xml=) 19 (=repeat_annotate_custom.xml=)
20 20
21 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 21 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.
22 22 ** TODO Summarize Annotation
23 This tool will create summary table from GFF annotation.
23 * test data 24 * test data
24 25
25 - ~test_assembly_1.fasta~ with ~test_db_1_satellites.fasta~ (include CLASS followed by double underscore - syntax 1) 26 - ~test_assembly_1.fasta~ with ~test_db_1_satellites.fasta~ (include CLASS followed by double underscore - syntax 1)
26 - ~test_assembly_2.fasta~ with ~test_db_2_RE_repeats.fasta~ (include full hierarchical classification) 27 - ~test_assembly_2.fasta~ with ~test_db_2_RE_repeats.fasta~ (include full hierarchical classification)
27 28