NAME

App::Egaz - Easy Genome Aligner

SYNOPSIS

egaz <command> [-?h] [long options...]
        --help (or -h)  show help
                        aka -?

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
     maskfasta: soft/hard-masking sequences in a fasta file
        multiz: multiz step by step
     normalize: normalize lav files
     partition: partitions fasta files by size
       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 stands for Easy Genome Aligner.

Caution: egaz lpcnam implements 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/0.2.8.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/0.2.8.tar.gz
# cpanm -nq https://github.com/wang-q/App-Egaz.git

CONTAINER

egaz has tons of dependencies, so the simplest way to use it is using a container system. Singularity 3.x is the preferred one.

# Pull and build the image
singularity pull docker://wangq/egaz:master

# Run a single command
singularity run egaz_master.sif egaz help

# Interactive shell
# Note:
#   * .sif is immutable
#   * $HOME, /tmp, and $PWD are automatically loaded
#   * All actions affect the host paths
#   * Singularity Desktop for macOS isn't Fully functional.
#       * https://github.com/hpcng/singularity/issues/5215
singularity shell egaz_master.sif

# With Docker
docker run -it --rm -v "$(pwd)"/egaz:/egaz wangq/egaz:master

EXAMPLE

Multiple genome alignments of Saccharomyces cerevisiae strains and other Saccharomyces species

Detailed steps https://github.com/wang-q/App-Egaz/blob/master/doc/Scer.md#detailed-steps

egaz 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

egaz template steps https://github.com/wang-q/App-Egaz/blob/master/doc/Scer-self.md#template-steps

AUTHOR

Qiang Wang <wang-q@outlook.com>

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.

CITATION

Yan Wang*, Xiaohui Liang*, Yuqian Jiang, Danjiang Dong, Cong Zhang, Tianqiang Song, Ming Chen, Yong You, Han Liu, Min Ge, Haibin Dai, Fengchan Xi, Wanqing Zhou, Jian-Qun Chen, Qiang Wang#, Qihan Chen#, Wenkui Yu#.

Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial.

eLife. 2022; 11: e79014.

DOI: https://doi.org/10.7554/eLife.79014

'*': These authors contributed equally to this work '#': For correspondence