[![Build Status](https://travis-ci.org/wang-q/App-Egaz.svg?branch=master)](https://travis-ci.org/wang-q/App-Egaz) [![Coverage Status](http://codecov.io/github/wang-q/App-Egaz/coverage.svg?branch=master)](https://codecov.io/github/wang-q/App-Egaz?branch=master) [![MetaCPAN Release](https://badge.fury.io/pl/App-Egaz.svg)](https://metacpan.org/release/App-Egaz) # NAME App::Egaz - Backend of **E**asy **G**enome **A**ligner # SYNOPSIS egaz [-?h] [long options...] -? -h --help show help Available commands: commands: list the application's commands help: display a command's help screen blastlink: link sequences by blastn blastmatch: matched positions by blastn in genome sequences blastn: blastn wrapper between two fasta files exactmatch: exact matched positions in genome sequences fas2vcf: list variations in blocked fasta file formats: formats of files use in this project lastz: lastz wrapper for two genomes or self alignments lav2axt: convert .lav files to .axt lav2psl: convert .lav files to .psl lpcnam: the pipeline of pairwise lav-psl-chain-net-axt-maf masked: masked (or gaps) regions in fasta files maskfasta: soft/hard-masking sequences in a fasta file multiz: multiz step by step normalize: normalize lav files partition: partitions fasta files by size plottree: use the ape package to draw newick trees prepseq: preparing steps for lastz raxml: raxml wrapper to construct phylogenetic trees repeatmasker: RepeatMasker wrapper template: create executing bash files Run `egaz help command-name` for usage information. # DESCRIPTION App::Egaz is the backend of **E**asy **G**enome **A**ligner. **Caution**: `egaz lpcnam` implement UCSC's chain-net pipeline, but some parts, e.g. `axtChain` don't work correctly under macOS. Use `egaz lastz`'s build in chaining mechanism (`C=2`) instead. # INSTALLATION cpanm --installdeps https://github.com/wang-q/App-Egaz/archive/0.0.11.tar.gz curl -fsSL https://raw.githubusercontent.com/wang-q/App-Egaz/master/share/check_dep.sh | bash cpanm -nq https://github.com/wang-q/App-Egaz/archive/0.0.11.tar.gz # cpanm -nq https://github.com/wang-q/App-Egaz.git # EXAMPLE - Multiple genome alignments of _Saccharomyces cerevisiae_ strains and other _Saccharomyces_ species - Detailed/alternative steps [https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md#detailedalternative-steps](https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md#detailedalternative-steps) - `egaz template` steps [https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md#template-steps](https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md#template-steps) - Self alignments of _S. cerevisiae_ reference strain S288c - Detailed steps [https://github.com/wang-q/App-Egaz/blob/master/doc/Scer-self.md#detailed-steps](https://github.com/wang-q/App-Egaz/blob/master/doc/Scer-self.md#detailed-steps) - `egaz template` steps [https://github.com/wang-q/App-Egaz/blob/master/doc/Scer-self.md#template-steps](https://github.com/wang-q/App-Egaz/blob/master/doc/Scer-self.md#template-steps) # AUTHOR Qiang Wang # LICENSE This software is copyright (c) 2018 by Qiang Wang. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.