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package App::Anchr; |
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use 5.010001; |
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use strict; |
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use warnings; |
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use App::Cmd::Setup -app; |
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our $VERSION = "0.4.3"; |
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=pod |
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=encoding utf-8 |
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=head1 NAME |
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App::Anchr - B<A>ssembler of B<N>-free B<CHR>omosomes |
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=head1 SYNOPSIS |
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anchr <command> [-?h] [long options...] |
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-? -h --help show help |
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Available commands: |
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commands: list the application's commands |
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help: display a command's help screen |
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anchors: selete anchors from k-unitigs or superreads |
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break: break long reads by anthors |
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contained: discard contained super-reads, k-unitigs, or anchors |
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cover: trusted regions in the first file covered by the second |
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dazzname: rename FASTA reads for dazz_db |
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dep: check or install dependances |
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group: group anthors by long reads |
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kunitigs: create k-unitigs from corrected reads |
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layout: layout anthor group |
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merge: merge overlapped super-reads, k-unitigs, or anchors |
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orient: orient overlapped sequences to the same strand |
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overlap: detect overlaps by daligner |
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overlap2: detect overlaps between two (large) files by daligner |
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quorum: Run quorum to discard bad reads |
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replace: replace IDs in .ovlp.tsv |
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restrict: restrict overlaps to known pairs |
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scaffold: scaffold anchors (k-unitigs/contigs) using paired-end reads |
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show2ovlp: LAshow outputs to ovelaps |
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trim: trim PE Illumina fastq files |
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Run C<anchr help command-name> for usage information. |
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=head1 DESCRIPTION |
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App::Anchr is tend to be an Assembler of N-free CHRomosomes. |
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=head1 INSTALLATION |
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cpanm --installdeps https://github.com/wang-q/App-Anchr/archive/0.3.2.tar.gz |
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curl -fsSL https://raw.githubusercontent.com/wang-q/App-Anchr/master/share/install_dep.sh | bash |
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curl -fsSL https://raw.githubusercontent.com/wang-q/App-Anchr/master/share/check_dep.sh | bash |
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cpanm -nq https://github.com/wang-q/App-Anchr/archive/0.3.2.tar.gz |
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# cpanm -nq https://github.com/wang-q/App-Anchr.git |
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=head1 AUTHOR |
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63
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Qiang Wang E<lt>wang-q@outlook.comE<gt> |
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65
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=head1 LICENSE |
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67
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This software is copyright (c) 2017 by Qiang Wang. |
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69
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This library is free software; you can redistribute it and/or modify |
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it under the same terms as Perl itself. |
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72
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=cut |
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1; |
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__END__ |