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# NAME

App::Anchr - **A**ssembler of **N**-free **CHR**omosomes

# SYNOPSIS

    anchr <command> [-?h] [long options...]
            -? -h --help  show help

    Available commands:

       commands: list the application's commands
           help: display a command's help screen

        anchors: selete anchors from k-unitigs or superreads
          break: break long reads by anthors
      contained: discard contained super-reads, k-unitigs, or anchors
          cover: trusted regions in the first file covered by the second
       dazzname: rename FASTA reads for dazz_db
            dep: check or install dependances
          group: group anthors by long reads
       kunitigs: create k-unitigs from corrected reads
         layout: layout anthor group
          merge: merge overlapped super-reads, k-unitigs, or anchors
         orient: orient overlapped sequences to the same strand
        overlap: detect overlaps by daligner
       overlap2: detect overlaps between two (large) files by daligner
         quorum: Run quorum to discard bad reads
        replace: replace IDs in .ovlp.tsv
       restrict: restrict overlaps to known pairs
       scaffold: scaffold anchors (k-unitigs/contigs) using paired-end reads
      show2ovlp: LAshow outputs to ovelaps
           trim: trim PE Illumina fastq files

Run `anchr help command-name` for usage information.

# DESCRIPTION

App::Anchr is tend to be an Assembler of N-free CHRomosomes.

# INSTALLATION

    cpanm --installdeps https://github.com/wang-q/App-Anchr/archive/0.3.2.tar.gz
    curl -fsSL https://raw.githubusercontent.com/wang-q/App-Anchr/master/share/install_dep.sh | bash
    curl -fsSL https://raw.githubusercontent.com/wang-q/App-Anchr/master/share/check_dep.sh | bash
    cpanm -nq https://github.com/wang-q/App-Anchr/archive/0.3.2.tar.gz
    # cpanm -nq https://github.com/wang-q/App-Anchr.git

# AUTHOR

Qiang Wang <wang-q@outlook.com>

# LICENSE

This software is copyright (c) 2017 by Qiang Wang.

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.