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1 # RepeatExplorer2 with TAREAN (Tandem Repeat Analyzer) #
2 -------------------------------------------------------------------------------
3 New version of RepeatExplorer with TAndem REpeat ANalyzer
4
5 ## Authors
6 Petr Novak, Jiri Macas, Pavel Neumann
7 Biology Centre CAS, Czech Republic
8
9 ## Change log
10
11 [link](CHANGELOG.md)
12
13
14
15 ## Instalation ##
16 To use RepeatExplorer without installation, We recommend to use our freely
17 available galaxy server at
18 [https://repeatexplorer-elixir.cerit-sc.cz](https://repeatexplorer-elixir.cerit-sc.cz).
19 This server is provided in frame of ELIXIR-CZ project. Additionally, the galaxy
20 server includs also additional tools useful data preprocessing, quality contraol
21 and genome annotation.
22
23 For command line version from standalone installation, follow the instruction below:
24
25
26 To download source using git command:
27
28 git clone https://bitbucket.org/petrnovak/repex_tarean.git
29 cd repex_tarean
30
31 We recommend to install dependencies using conda (conda can be installed using [miniconda](https://docs.conda.io/en/latest/miniconda.html)). The required environment can be prepared using command:
32
33 conda env create -f environment.yml
34
35 activate prepared environment using:
36
37 conda activate repeatexplorer
38
39 In the `repex_tarean` direcory compile source and prepare databases using:
40
41 make
42
43 Support for 32-bit executables is required. If you are using Ubuntu distribution you can add 32-bit support by running:
44
45 sudo dpkg --add-architecture i386
46 sudo apt-get update
47 sudo apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386
48
49
50 to verify installation you can run clustering on example data:
51
52 ./seqclust -p -v tmp/clustering_output test_data/LAS_paired_10k.fas
53
54
55 ## Protein databases
56
57 Repeatexplorer2 utilize REXdb database of protein domains for repeat annotation and classification. Structure of database is described on [http://repeatexplorer.org/](http://repeatexplorer.org/). Current version of database for repeatexplorer is fetched from bitbucket repository [https://bitbucket.org/petrnovak/re_databases]https://bitbucket.org/petrnovak/re_databases() during compilation using make command
58
59
60 ## RepeatExplorer command line options
61
62 usage: seqclust [-h] [-p] [-A] [-t] [-l LOGFILE] [-m {float range 0.0..100.0}]
63 [-M {0,float range 0.1..1}] [-o {float range 30.0..80.0}]
64 [-c CPU] [-s SAMPLE] [-P PREFIX_LENGTH] [-v OUTPUT_DIR]
65 [-r MAX_MEMORY] [-d DATABASE DATABASE] [-C] [-k]
66 [-a {2,3,4,5}]
67 [-tax {VIRIDIPLANTAE3.0,VIRIDIPLANTAE2.2,METAZOA2.0,METAZOA3.0}]
68 [-opt {ILLUMINA,ILLUMINA_DUST_OFF,ILLUMINA_SHORT,OXFORD_NANOPORE}]
69 [-D {BLASTX_W2,BLASTX_W3,DIAMOND}]
70 sequences
71
72 RepeatExplorer:
73 Repetitive sequence discovery and clasification from NGS data
74
75
76
77 positional arguments:
78 sequences
79
80 optional arguments:
81 -h, --help show this help message and exit
82 -p, --paired
83 -A, --automatic_filtering
84 -t, --tarean_mode analyze only tandem reapeats without additional classification
85 -l LOGFILE, --logfile LOGFILE
86 log file, logging goes to stdout if not defines
87 -m {float range 0.0..100.0}, --mincl {float range 0.0..100.0}
88 -M {0,float range 0.1..1}, --merge_threshold {0,float range 0.1..1}
89 threshold for mate-pair based cluster merging, default 0 - no merging
90 -o {float range 30.0..80.0}, --min_lcov {float range 30.0..80.0}
91 minimal overlap coverage - relative to longer sequence length, default 55
92 -c CPU, --cpu CPU number of cpu to use, if 0 use max available
93 -s SAMPLE, --sample SAMPLE
94 use only sample of input data[by default max reads is used
95 -P PREFIX_LENGTH, --prefix_length PREFIX_LENGTH
96 If you wish to keep part of the sequences name,
97 enter the number of characters which should be
98 kept (1-10) instead of zero. Use this setting if
99 you are doing comparative analysis
100 -v OUTPUT_DIR, --output_dir OUTPUT_DIR
101 -r MAX_MEMORY, --max_memory MAX_MEMORY
102 Maximal amount of available RAM in kB if not set
103 clustering tries to use whole available RAM
104 -d DATABASE DATABASE, --database DATABASE DATABASE
105 fasta file with database for annotation and name of database
106 -C, --cleanup remove unncessary large files from working directory
107 -k, --keep_names keep sequence names, by default sequences are renamed
108 -a {2,3,4,5}, --assembly_min {2,3,4,5}
109 Assembly is performed on individual clusters, by default
110 clusters with size less then 5 are not assembled. If you
111 want need assembly of smaller cluster set *assmbly_min*
112 accordingly
113 -tax {VIRIDIPLANTAE3.0,VIRIDIPLANTAE2.2,METAZOA2.0,METAZOA3.0}, --taxon {VIRIDIPLANTAE3.0,VIRIDIPLANTAE2.2,METAZOA2.0,METAZOA3.0}
114 Select taxon and protein database version
115 -opt {ILLUMINA,ILLUMINA_DUST_OFF,ILLUMINA_SHORT,OXFORD_NANOPORE}, --options {ILLUMINA,ILLUMINA_DUST_OFF,ILLUMINA_SHORT,OXFORD_NANOPORE}
116 -D {BLASTX_W2,BLASTX_W3,DIAMOND}, --domain_search {BLASTX_W2,BLASTX_W3,DIAMOND}
117 Detection of protein domains can be performed by either blastx or
118 diamond" program. options are:
119 BLASTX_W2 - blastx with word size 2 (slowest, the most sesitive)
120 BLASTX_W3 - blastx with word size 3 (default)
121 DIAMOND - diamond program (significantly faster, less sensitive)
122 To use this option diamond program must be installed in your PATH
123
124
125
126 ## Galaxy toolshed
127 TODO
128
129 ## Reproducibility
130 To make clustering reproducible between runs with the
131 same data, environment variable PYTHONHASHSEED must be set:
132
133 export PYTHONHASHSEED=0
134
135 ## Disk space requirements
136 Large sqlite database for temporal data is created in OS specific temp directory- usually /tmp/
137 To use alternative location, it is necessary specify `TEMP` environment variable.
138
139 ## CPU and RAM requirements
140
141 Resources requirements can be set either from command line arguments `--max-memory` and `--cpu` or
142 using environment variables `TAREAN_MAX_MEM` and `TAREAN_CPU`. If not set, pipeline use all
143 available resources
144
145 ## How cite
146
147 If you use RepeatExplorer for general repeat characterization in your work please cite:
148
149 - [Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next generation sequence read. Bioinformatics 29:792-793](http://bioinformatics.oxfordjournals.org/content/29/6/792)
150
151 or
152
153 - [Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11 :37](http://www.biomedcentral.com/1471-2105/11/378)
154
155 If you use TAREAN for satellite detection and characterization please cite:
156
157 - [Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acid Research](https://doi.org/10.1093/nar/gkx257)
158