App::Anchr - Assembler of N-free CHRomosomes
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.
App::Anchr is tend to be an Assembler of N-free CHRomosomes.
cpanm --installdeps https://github.com/wang-q/App-Anchr/archive/0.5.4.tar.gz
# cpanm --installdeps --verbose --mirror-only --mirror http://mirrors.ustc.edu.cn/CPAN/ https://github.com/wang-q/App-Anchr.git
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/0.5.4.tar.gz
# cpanm -nq https://github.com/wang-q/App-Anchr.git
Qiang Wang wang-q@outlook.com
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.