.\" https://raw.github.com/udo-stenzel/anfo/master/man/anfo.1
.\" ANFO short read aligner
.\" (C) 2009 Udo Stenzel
.\"
.\" This program is free software; you can redistribute it and/or modify
.\" it under the terms of the GNU General Public License as published by
.\" the Free Software Foundation; either version 3 of the License, or (at
.\" your option) any later version.  See the COPYING file for details.

.\" Process this file with
.\" groff -man -Tascii patman.1
.\"
.TH ANFO 1 "OCTOBER 2009" Applications "User Manuals"
.SH NAME
anfo \- find best alignment of short reads to database
.SH SYNOPSIS
.B anfo [
.I option
.B |
.I file
.B ... ]
.SH DESCRIPTION
.B anfo
aligns (short) sequencing reads to a (gigabase sized) database.  It uses
a heuristic seeding method, but then applies a genuine aligner that
allows gaps, understands damage patterns in ancient dna and produces an
easy to interpret score.

Input files can be any variety of FastA or FastQ files, or a native
.B anfo
binary file, optinally compressed using 
.BR gzip or bzip2 .
The file format is automatically recognized and other formats may be
added.


.SH OPTIONS
.IP "-V, --version"
Print version number and exit.

.IP "-o file, --output file"
Write output to 
.IR file ". " file
will be written in the native
.B anfo
binary format, which can be operated upon using
.B anfo-tool
or the bindings to
.BR guile .

.IP "-c conffile, --config conffile"
Read configuration from 
.IR conffile .
This file configures which indices are used, and by extension to which
genomes an alignment is made, what parameters to use in the aligner and
can set paths.  See the example file.

.IP "-p num, --threads num"
Start
.I num
threads for alignment.  One such thread per processor core is usually
best.

.IP "-x num, --ixthreads num"
Start 
.I num
threads for indexing.  Indexing normally uses less cpu power than
alignment, so fewer indexers than aligners is normally best.

.IP "--solexa-scale"
When reading FastQ files, use the Solexa scale (log-odds-ratios) instead
of the standard Phread scale (probabilities).  If you use
Solexa/Illumina sequencers, refer to your documentation whether you need
this.  Else you don't.

.IP "--fastq-origin ori"
Set origin for FastQ decoding to
.IR ori .
The standard and default is 33, but it must be set to 64 for some
versions of the Solexa/Illumina software.  If you use Solexa/Illumina
sequencers, refer to your documentation whether you need this.  Else you
don't.

.IP "-q, --quiet"
Suppress all output except fatal errors.

.IP "-v, --verbose"
Print a progress indicator during operation.


.SH ENVIRONMENT
.IP ANFO_PATH
Colon separated list of directories searched for genome and index files.

.SH FILES
.I /etc/popt
.RS
The system wide configuration file for
.BR popt (3).
.B anfo
identifies itself as "anfo" to popt.
.RE

.I ~/.popt
.RS
Per user configuration file for
.BR popt (3).
.RE

.I /usr/share/doc/anfo/example/*.cfg
.RS
Example configuration files to be used with 
.BR anfo .
.RE

.SH BUGS
None known.

.SH AUTHOR
Udo Stenzel <udo_stenzel@eva.mpg.de>

.SH "SEE ALSO"
http://bioinf.eva.mpg.de/anfo

.BR anfo-tool "(1), " anfo-sge "(1), " fa2dna "(1), " dnaindex "(1), " popt "(3), " fasta (5)